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.

The Pentagon which manges the military relations between the two countries has expressed concerns over moves by Egypt’s ruling generals to stay in power despite a presidential vote while it urged the Egyptian military to relinquish power to civilian-elected authorities and to respect the universal rights of the Egyptian people and the rule of law.

The military power grab poses a dilemma for the  Obama administration, which publicly backed the revolution that ousted longtime leader Hosni Mubarak last year but also sees the Egyptian army as a crucial regional security partner, according to Al Jazeera. 

The Brotherhood has called on people to demonstrate against what it says is a “military coup” by the ruling generals, as the country awaits the final tally from the election expected to come out on June 21. All of the results announced on Sunday night are unofficial.

But shortly before the final result of the elections the generals who run the country stirred controversy by issuing new rules in a constitutional declaration demonstrating the president’s powers that made clear power remains within the hands of the army.

According to a decree issued on Sunday night, the military council will hold authority over the budget and the legislative process until a new parliament is elected, according to Al Arabiya. 

The decree also limits the new president’s powers who can only declare war if approved by the military council.

Sameh Ashour, the head of SCAF’s advisory council, said the incoming president would probably have a short term, and would be replaced after a new constitution was drafted, according to Al Jazeera. 

“With 97% of polling stations reporting, Morsi ahead of shafiq by 1.2 million votes”,  Muslim Brotherhood said in a brief statement on facebook.

The latest statements from the Muslim Brotherhood candidate reveal Mursi has garnered 53 percent of the vote to 47 percent for his rival, ex-prime minister Ahmed Shafiq, with the ballots from nearly all of the country’s 13,000 polling stations counted, according to Al Arabiya.

Supporters chanted “down with military rule” after the results were announced while thousands rejoiced in Tahrir square to celebrate Mursi’s victory.

All of the results announced on Sunday night are unofficial and a final tally will not come out until later this week on June 21.

Representatives from Ahmed Shafiq’s campaign said that they would not accept the Brotherhood’s tally, and would wait for final results.

Turnout was lower than during the first round of voting in May, according to the secretary-general of the presidential election commission.

But shortly before the final result the generals who have run the country stirred controversy by issuing new rules in a constitutional declaration demonstrating the president’s powers that made clear real power remains with the army.

Those powers are quite limited: He may declare war, for example, only after seeking SCAF’s approval. The decree also reminds the president that he can call on the military to quell “unrest” inside the country, according to Al Jazeera.

SCAF dissolved parliament last week following a ruling by the supreme court, which found the legislature illegitimate. With the legislature gone, the generals reasserted control over the legislative process, and over the country’s budget.

The decree issued on Sunday promises new legislative elections, but not until a new constitution has been drafted. Before it was dissolved, the parliament appointed a 100-member assembly to draft that constitution; it will be allowed to continue its work, though if it runs into “obstacles”, SCAF will appoint a replacement, Al Jazeera rpeorted.

The Muslim Brotherhood was quick to condemn the decree, calling it “null and unconstitutional” in a brief statement on Twitter.