When the army ousted Morsi on 3 July, Reporters Without Borders urged the new interim government to respect its initial route map by quickly moving to “a new constitution that fully respects human rights, including freedom of information, and to free and democratic presidential and parliamentary elections with respect for pluralism.”

Since 3 July, a total of five journalists have been killed, 80 journalists have been arbitrarily detained (with seven still held) and at least 40 news providers have been physically attacked by the police or by pro-Morsi or pro-army demonstrators.

These violations of freedom of information have taken place in a highly polarized political environment that has made the situation extremely difficult and dangerous for journalists.

Reporters Without Borders said it condemns the climate of violence and political persecution in which both local and foreign journalists now have to operate in Egypt.

“It is unacceptable that journalists are continually being targeted,” Reporters Without Borders said. “Reporters must be able to work without their lives being put in danger, regardless of the political fault lines. We deplore the passivity of the new Egyptian authorities and we urge them to react quickly by taking concrete measures to guarantee journalists’ safety and respect for freedom of information.”

Reporters Without Borders points out that media coverage of the events taking place in Egypt is essential for understanding the complexity of the situation on the ground.

Meanwhile, Egyptian security forces continue to detain and harass journalists working for news outlets critical of the military-led government, particularly Al-Jazeera and its affiliates, according to the Committee to Protect Journalists(CPJ) . Journalists also still face physical threats from protesters, as tensions persist between the government and supporters of ousted President Mohamed Morsi.

The Ministry of Investment on Thursday August 29, 2013 said it would ban Al-Jazeera Mubashir, the network’s Egyptian affiliate, because it lacked the required legal permits, according to news reports. The statement accused the channel of “spreading lies and rumors damaging to Egyptian national security and unity.” Today, the Ministry of Interior issued a statement saying it had confiscated two broadcasting cars and equipment from Al-Jazeera Mubashir.

On Tuesday August 27, Egyptian security forces detained without charge four staff of Al-Jazeera English, including correspondent Wayne Hay, cameraman Adil Bradlow, and producers Russ Finn and Baher Mohammed, the station reported. Al-Jazeera Arabic correspondent Abdullah al-Shami and Al-Jazeera Mubashir cameraman Mohamed Bader had been arrested earlier this month while covering protests and held under charges of “threatening national security” and “possessing weapons,” respectively.

Six of the 10 journalists in custody in Egypt are from Al-Jazeera and its affiliates, according to CPJ research.

“I deplore the deaths of Ahmed Abdel Gawad, Mosab Al-Shami and Tamer Abdel Raouf,” said the Director-General of the UN Educational, Scientific and Cultural Organization (UNESCO), Irina Bokova, calling on Egyptian authorities “to do everything possible to ensure the security of media workers.”

Ms. Bokova expressed her distress and concern over the violence directed against the media in Egypt, where five media professionals have been killed while carrying out their duties in the span of a few days.

According to Reporters Without Borders, Mr. Gawad, a reporter for the Egyptian daily Al-Akhbar, and Mr. Al-Shami, a photojournalist for Rassd News Network, were killed on 14 August while covering demonstrations in the capital, Cairo. Both died from gunshot injuries.

Mr. Raouf was the regional director of Egypt’s Al-Ahram newspaper. He was shot dead at a vehicle checkpoint in Damanhur, in the Beheira Governorate in northern Egypt, on 19 August. Another journalist in the car, Hamed Al-Barbari, was injured.

Ms. Bokova also condemned yesterday the murder of Pakistani journalist Haji Abdul Razzak and Guatemalan journalist Carlos Alberto Orellana Chávez.

Mr. Razzak, 35, was a reporter for the Urdu-language newspaper Daily Tawar. His mutilated body was found in the city of Karachi last Wednesday. He had been reported missing since 24 March.

A broadcast journalist in Guatemala, Mr. Orellana Chávez hosted a news programme on Optimo 23 cable television after having directed Radio Victoria for over 25 years. According to Reporters Without Borders, he was shot down as he was driving to work some 50 kilometres from Mazatenango, the provincial capital of Suchitepequez, in the south of the country.

Ms. Bokova called on Pakistani and Guatemalan authorities “to do all in their power” to investigate the killings and shed light on these heinous crimes.

Mubarak was taken from Cairo’s Tora prison by medical helicopter on Thursday, following a court ruling which ordered his release. A medical helicopter then carried Mubarak to the Maadi Medical Hospital afternoon, according to local media.

Interim Prime Minister Hazem El-Beblawi has ordered Mubarak be placed under house arrest, according to AFP, with his travel ban remaining in effect.

Although Mubarak is released from prison he still faces charges of being involved in the killing of peaceful protesters in the 2011 uprising.

Mubarak was convicted last year of corruption and involvement in the murder of protesters during an uprising where Egyptians took to Tahrir Square for 18 days to demand his ouster.

Meanwhile, supporters of Egypt’s ousted president Mohamed Mursi called on the Egyptian people to protest against the army Friday.

Egypt has witnessed unprecedented violent clashes since security forces dispersed two major pro-Morsi sit-ins in the country a week ago.

Until now, almost 1,000 people have been killed across the country, according to Al Jazeera.

Islamist groups in Egypt have been accusing Mursi’s ouster in early July as a “military coup”.

In July this year, Mohamed Morsi, the first democratically elected president, was deposed by the armed forces after only one year in office.

Security forces moved in on two Cairo protest camps set up by supporters of Egypt’s ousted president Mohamed Morsi leaving scores dead on Wednesday.

The latest updates on the death toll vary widely

A death tally by AFP says 124 were killed at the Rabaa Al-Adawiya sit-in alone while Aljazeera’s correspondent counted 94 bodies in Rabaa al-Adawiya’s makeshift hospital. The Health Ministry has put the figure at 15 people killed.

However, the Muslim Brotherhood said the death toll was as high as 2,200, with about 10,000 injured.

Meanwhile, the security crackdown has sparked global outrage.

The EU has issued a statement urging all sides to exercise maximum restraint.

“Confrontation and violence are not the way forward,” said Peter Stano, spokesman for EU foreign affairs chief Catherine Ashton. “Reports about deaths and injuries in this respect are extremely worrying.”

Iran also condemned what it called a “massacre” as police moved on Wednesday to clear protests in Cairo by supporters of ousted president Mohamed Morsi, Fars news agency reported.

Qatar, a main backer of the pro-Morsi Muslim Brotherhood, issued a similar message.

“Qatar strongly denounces the means by which peaceful protesters in Rabaa al-Adawiya camp and Al-Nahda square have been dealt with and which led to the killing of several unarmed innocent people among them,” a foreign ministry spokesman said in a statement published on the official QNA agency.

There was no immediate reaction from the United States to Wednesday’s bloodshed.

Egyptians braced for a showdown after Friday prayers as Gen. Abdel Fattah al-Sisi, the head of Egypt’s military, called for mass demonstrations Friday to support the country’s armed forces.

On the other hand, people joined thousands of Mursi supporters amid calls by the Muslim brotherhood for a million-man march under the title “bringing down the coup.”

Pro-Mursi supporters have been rallying against his overthrow and holding demonstrations since July 3.

In a related development on Friday, Egypt’s state prosecutor has ordered that ousted President Mohamed Mursi be detained for questioning over suspected cooperation with Hamas, official MENA news agency reported.

Meanwhile, UN chief Ban Ki-Moon urged the interim authorities to release Mursi and Muslim Brotherhood leaders currently in detention or have their cases reviewed transparently without delay, deputy UN spokesman Eduardo del Buey said.

Speaking at a press conference in Geneva today, the spokesperson for UN High Commissioner for Human Rights Navi Pillay stressed that it is extremely important that security forces in Egypt do not resort to excessive use of force.

The crisis in the country escalated earlier this month, resulting in the Egyptian military deposing President Mohamed Mursi amid widespread protests in which dozens of people were killed and wounded. The Constitution was then suspended and an interim government set up.

The organization has gathered testimonies from detainees who said that they were beaten upon arrest, subjected to electric shocks or hit with rifle butts.

The Egyptian authorities must respect the right to due process for those who have been rounded up and are facing accusations of inciting or participating in violence in the last two weeks. Allegations of ill-treatment must be investigated urgently.

“At this time of extreme polarization and division, it is more important than ever that the office of the Public Prosecutor demonstrates that it’s truly independent and not politicized,” said Hassiba Hadj Sahraoui, Deputy Middle East and North Africa Programme Director at Amnesty International. “These cases risk being seen as mere retribution rather than justice.”

Since the news of Mursi’s ousting on 3 July, lawyers have told Amnesty International that more than 660 men have been arrested in Cairo alone, including prominent leaders of the Muslim Brotherhood and its political wing, the Freedom and Justice Party (FJP). Many were arrested on 8 July during the violence around the Republican Guard Club, which left at least 51 Morsi supporters dead.

While release orders were eventually issued for some 650 suspects, lawyers have told the organization that an unknown number remain in detention due to their inability to pay bail ranging from 1,000 to 5,000 Egyptian pounds (US$140-US$700). The whereabouts of the deposed President and his team of aides are still unknown.

Amnesty International fears that their conditions of detention may amount to an enforced disappearance. Family members who have asked have been denied information on their relative’s whereabouts and fate, and they appear not to have been brought before a judge or given access to a lawyer

“Establishing trust in the justice system will be impossible if only supporters of Mursi and the Muslim Brotherhood are targeted while security forces are absolved of responsibility for unlawful killings and their failure to protect protesters from violence,” said Hassiba Hadj Sahraoui, Deputy Middle East and North Africa Programme Director at Amnesty International.

“Everyone has the right to due process, no matter what the authorities think of their political affiliation or their position. Mohamed Morsi and his team, like anyone, should be granted their basic rights, including immediate access to their lawyers and family.”

Under international law, all detained suspects must be released or promptly charged with a recognizable criminal offence. Anyone deprived of their liberty should also have the right to challenge the lawfulness of their detention before a judge, as well as access to lawyers and their families, and receive any medical treatment that they might require. Lawyers must be permitted to assist their clients unimpeded.

Amnesty International urges the Egyptian authorities to launch full investigations into reports of detainees being beaten and ill-treated, particularly upon arrest, in the vicinity of the Republican Guard Club. This including being hit with rifle butts and given electric shocks. They also said that at police stations they were interrogated while blindfolded by men they believed to be intelligence officials from the National Security Agency, a practice that is eerily reminiscent of Mubarak-era tactics. Newly released detainees also complained about not being allowed to call their families or lawyers.

With at least nine senior Muslim Brotherhood leaders and supporters already detained, arrest warrants have also been issued for other prominent figures in the Muslim Brotherhood, including the group’s spiritual guide. The Muslim Brotherhood’s chief lawyer, Abdelmonim Abdelmaqsoud, has also been detained in Tora Prison, south of Cairo.

“The onus is on the prosecution and the authorities to charge and provide evidence to support the accusations against them,” said Hassiba Hadj Sahraoui. “Without evidence that can be tested in court it is yet another crackdown on the Muslim Brotherhood.”

Directly after the army announced the ousting on 3 July, at least six pro-Morsi television stations were taken off the air and then had their studios raided. The following day the FJP announced that the state’s printing press refused to print the party’s newspaper. On Sunday the Public Prosecution froze the assets of 14 men associated with the Muslim Brotherhood and parties supporting them.

At least 51 Morsi supporters were killed Monday during clashes outside the Republican guard headquarters.

“Despite claims by the military that protesters attacked first during clashes on Monday and that no women and children were injured, first hand accounts collected by Amnesty International paint a very different picture. Even if some protesters used violence, the response was disproportionate and led to the loss of life and injury among peaceful protesters,” said Hassiba Hadj Sahraoui, Middle East and North Africa Deputy Director at Amnesty International.

The army and Interior Ministry said yesterday that the violence followed an attack by protesters around the Republican Guard Club, and announced that a military officer and two members of the security forces were killed.

However, accounts collected from eyewitnesses contradict this version of events. Amnesty International has visited morgues, hospitals and sites of violence in Cairo and Alexandria to gather testimonies from injured protesters and relatives of victims. Its findings suggest the use of disproportionate force by the security forces, including intentional lethal force. Many of those killed and injured had been shot in the head and upper body with shotgun pellets and live ammunition.

“The Egyptian authorities must end the military and police’s use of grossly disproportionate force. Even when individual protesters use violence, the army must respond proportionately, without killing and injuring those not endangering the lives of the security forces or others. They must ensure an investigation which all sides see as independent and impartial is promptly conducted to ensure any alleged army abuses are not covered up”.

“The Egyptian authorities must also ensure that proper autopsy and medical reports are issued to facilitate thorough investigations and ensure access to justice and reparations.”

Amnesty International’s fears of further bloodshed are heightened by statements by Muslim Brotherhood leaders vowing to continue protesting until the former President is reinstated, calling on their supporters to “rise up” and “resist”, despite the ongoing deaths and injuries.

“As politicians squabble over who started the violence, it’s clear that unless the security forces are reined-in and clear orders given on the use of force we’re looking at a recipe for disaster.”

A woman in her forties who was wounded on Monday said the violence began at as she finished prayers beside a tent housing women and children.

“I saw men running towards us, then the teargas started falling. I did not know what to do or where to take the children. I couldn’t go back to the tents because we would suffocate, and I didn’t know where to run because of the shooting…There were shots and teargas coming from all directions…There were men lying on the ground in pools of blood in front of me, I just stayed there under the tree praying…I thought that was it,” she said. Eventually, she managed to escape down a side street.

Amnesty International interviewed several other women who had shotgun pellet wounds in the upper body including the back, and a child at a Cairo hospital with wounds in his head, face and legs.

The deaths Monday  followed shootings on 5 July, when security forces shot dead four people during protests in front of the Republican Guard.

The organization also found that security forces had intervened too late or not at all during clashes between pro and anti Morsi supporters in Cairo and Alexandria on 5 July leading to a loss of life on both sides.

At least eight people died during clashes between rival camps that lasted around five hours in Tahrir Square and the district of al-Manial in Cairo on Friday, with the security forces absent from the scene.

In Alexandria on Friday, at least 17 were killed in the Sidi Gaber area. Security forces arrived on the scene after some people had already been killed. Mohamed Badr al-Din, a local resident, was stabbed and thrown from a roof by Morsi supporters.

“It is the responsibility of the security forces to maintain security and protect lives. However, instead of preventing further bloodshed they appear to have contributed to it by using excessive force and ignoring the people’s pleas for help,” Hassiba Hadj Sahraoui said. “Those who violently attack their political opponents should be held to account, whatever their political affiliation.”

“The ‘National Alliance in Support of Electoral Legitimacy’ (NASEL) appealed to the masses of the Egyptian people to mobilize in peaceful mass marches in all liberty squares and streets of Egypt, to be started from all mosques, after Friday prayers, to reject the heinous coup against popular will,” the alliance said in a statement.

NASEL said that it feels rising public anger and the imminent danger threatening the nation as a result of the unprecedented military coup d’état against legitimacy derived from the will of the people and the January 25 Revolution.

Moreover, NASEL stressed “categorical rejection of the terror and violence dealt by the new police state authorities, which began from the first moment the coup was announced with all forms of repression, restriction of freedoms, closure of satellite TV channels – especially Islamist ones, restricting the freedom of the media, the arrest of politicians, and framing innocent people,” it added.

The military  shut down four Islamist TV stations, banned the Muslim Brotherhood’s newspaper and raided the office of Al-Jazeera in Egypt, bringing an outcry Thursday from rights groups.

Rights groups said the moves appeared to be an attempt to intimidate pro-Mursi media and shut off their viewpoints, according to AP.

The military’s move came hours after the announcement of the military chief that Mursi had been removed.

In a statement, the Brotherhood said the shutdowns were a return to the “repressive” policies of Egypt’s “dark … ages.”

Mursi, his aides, and Muslim Brotherhood officials have been placed under house arrest after Mursi was ousted from power in Egypt, according to Reuters.

Meanwhile, Adly Mansour, the head of the Supreme Constitutional Court, with which Morsi had repeated confrontations, was sworn in as interim president on Thursday.

At least 16 people have been killed and hundreds wounded in clashes across Egypt since Mursi’s overthrow.

In a televised statement on Wednesday by Army chief General Abdel Fattah al-Sisi, he announced that the constitution would be suspended, and early elections would take place.

The general, who had issued a 48-hour ultimatum to Mr. Morsi on Monday to respond to resolve the political crisis in the country said the president’s defiant response in a televised address on Tuesday had failed “to meet the demands of the masses of the people.” And calls by the armed forces for reconciliation.

The general’s announcement came after the armed forces had deployed tanks and troops in Cairo and other cities where pro-Mursi crowds were massing, according to Al Ahram English news website.

Mursi will be replaced by the chief justice of constitutional court, Adly Mansour. He will be sworn in on Thursday.

Shortly before the army’s announcement Mursi remained defiant that his presidency was still valid and refuseed to bow down to what he called an illegal coup.

Ahmed al-Tayeb, Grand Sheikh of Al-Azhar, Cairo’s ancient seat of Muslim learning, and Pope Tawadros, the head of the Coptic Church, both backed the army’s decision and made brief statements following the announcement, Al Jazeera reported.

“We are following with great concern the extremely tense situation in Egypt and wish to convey a strong message of solidarity and support to the Egyptian people,” the Spokesperson for the Office of the UN High Commissioner for Human Rights (OHCHR), Rupert Colville, told reporters in Geneva.

“We call on the President of Egypt to listen to the demands and wishes of the Egyptian people […] and to address key issues raised by the opposition and civil society in recent months, as well as to heed the lessons of the past in this particularly fragile situation.”

Egypt has been undergoing a democratic transition following the toppling of President Hosni Mubarak two years ago in the wake of mass protests similar to those seen in other parts of the Middle East and North Africa as part of what had been called the “Arab Spring.”

Protests have been taking place in various cities in recent days, with protesters reportedly calling for the resignation of President Mohamed Mursi.

At least 20 die in clashes between president’s supporters, opponents on Tuesday and early hours of Wednesday, according to Al Ahram news website.

On Monday, the Egyptian Armed Forces gave all parties involved in the ongoing political impasse until Wednesday 17:00 (Cairo time) to end their differences.

Should they fail to do so, the armed forces warned that it would issue its own “roadmap” for Egypt’s political future.

Mursi, meanwhile, delivered a speech Tuesday night in which he defied opposition calls to step down.

Yesterday, the UN Secretary-General repeated his call for all parties to uphold the law, while respecting the right to demonstrate peacefully. In particular, he underlined that this right must be extended to female demonstrators, given the concerns over the high number of reports of sexual assaults.