Presidential spokesman Yasser Ali said Mursi had appointed Tantawi as his adviser. Mursi also decreed that Abdul-Fatah al-Sessi would replace Tantawi as defense minister and the general commander of the army.

The chief of the army staff, Sami Anan, was appointed as a presidential adviser while Lieutenant-General Sidki Sayed Ahmed was named as Anan’s replacement.

Besides Tantawi and Anan, Morsi also ordered the retirement of the commanders of the navy, air defence and air force.

In an address to the nation on Sunday evening, Mursi said that his move was not directed at individuals.

”The decisions I took today were not meant ever to target certain persons, nor did I intend to embarrass institutions, nor was my aim to narrow freedoms,” he said, Al Jazeera reported.

“I did not mean to send a negative message about anyone, but my aim was the benefit of this nation and its people.

When Hosni Mubarak was ousted in a popular uprising in February 2011 Mubarak transferred authority to the Supreme Council of the Armed Forces, headed by the Tantawi, making him the de facto head of state until elections brought the President Mursi’s Muslim Brotherhood to power this year.

Relations between the military and the Muslim Brotherhood have been tense since the downfall of former President Hosni Mubarak.

The move comes as Egypt’s freshly-elected government faces criticism for unrest in the northern Sinai region, where militants attacked a border post last week, killing 16 troops.

Hours after holding talks with Clinton Egypt’s army chief, Field Marshal Hussein Tantawi said on Sunday the military will not let “one group” dominate the country, in an apparent reference to the Brotherhood.

“Egypt will not fall. It is for all Egyptians and not just one group… The armed forces will not allow it,” Tantawi said in statements carried by the official MENA news agency according to Al Arabiya.

Tensions between Egypt’s newly elected president and its ruling generals, who took interim power after former President Hosni Mubarak was ousted in an uprising against his rule last year, have risen since the military council stripped Mursi of some of his powers and granted itself legislative authority after the court ordered the dissolution of parliament.

Last week, Mursi ordered parliament to reconvene, in defiance of a military decision to dissolve it after the country’s top court ruled it illegitimate.
 Mursi’s decision was seen as a power struggle between Egypt’s first civilian leader and the ruling generals who want to stay in power even after they transferred control on June 30.

 But on Wednesday, Mursi said he would respect a court ruling overturning his decree.

During her visit, Clinton urged the military to help smooth the country’s full transition to democracy.

 Clinton has repeatedly called on the military to respect the results of the elections and told a news conference her talks with Tantawi would focus on “working to support the military’s return to a purely national security role.”

Saad el-Katatni, parliament speaker and Muslim brotherhood member, said he received a call from tussein Tantawi,head of Egypt’s ruling military council, notifying him about a reshuffle within 48 hours.

A source quoted in Al-Ahram’s Arabic-language website described the  reshuffle as “limited,” saying it would include new ministers from Islamist-oriented and other parties currently represented in Parliament.

The Muslim Brotherhood-led parliament, which seated three months ago, has been demanding it be allowed to form a cabinet to replace the military-appointed one it accuses of inefficiency.

The ruling generals, who have the power to sack the government, have resisted the calls and hinted at times that they will not allow the Brotherhood to dominate the country.

That resistance has also prompted the suspension of parliament sessions.

The parliament’s decision followed a night of violence marked with protests outside the defense ministry in the Egyptian capital to call for an end to military rule, according to Aljazeera.

The head of Egypt’s election commission on April 14 disqualified 10 candidates, amongst them  the Muslim Brotherhood’s Khairat al-Shater and the former president’s intelligence chief Omar Suleiman, while Salafist candidate Hazem Abu Ismail’s nomination was rejected because his mother had taken joint US citizenship.

The first round of the presidential election is scheduled for May 23 and 24 and a run-off on June 26-17 if necessary, while the interim military leadership has promised to hand power to an elected civilian president by the end of June.