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The impartiality of the courts is undermined because they are stocked with judges appointed by the autocratic former president Hosni Mubarak, whose regime was openly hostile to the Muslim Brotherhood.

Mubarak’s almost three decades in power were brought to an abrupt end by the Arab Spring uprising in February 2011. He has been sentenced to life in prison on charges of premeditated murder of peaceful protesters during the revolution.

“On one hand the Brotherhood looks like it is not respecting the rule of law, but on the other hand should they be respecting the ruling of a judicial establishment that is out to get them?” said Mr. Hamid.

“An argument can be made that Morsi was within his rights to reinstate parliament because he wasn’t reversing the Supreme Constitutional Court’s decision, he was reversing the SCAF’s executive decision to dissolve parliament. That distinction is important,” he added.

Mr. Morsi’s defiance of the military order is seen by some analysts as an act by a man determined to assert his authority.

No pushover president

“There was a growing conventional wisdom that this was going to be a weak, semi-ceremonial president,” said Mr. Hamid. “But now Morsi has shown he is not going to be a pushover president.”

However, in a sign that Mr. Morsi may not put up too stiff a fight to reinstate parliament, the presidential decree issued this week also stated that new parliamentary elections will be held within 60 days of the ratification of a new constitution.

It is Egypt’s future constitution that lies at the heart of the power struggle.

The military handed over executive powers to Mr. Morsi when the new president took the oath of office on June 30. It has retained legislative powers until a constitution is drafted and a new parliament elected.

“One of the important prizes right now is the control of the state, and the other is the writing of the new constitution and who is going to control that and what it says,” said Ms. Dunne.

Eric Trager, an Egypt analyst at the Washington Institute for Near East Policy, added, “We need to prepare for the likelihood that Egypt’s transition will continue for a really long time and its key storyline will be the battle between the Brotherhood and the military. This is Round 1 of a boxing match.”

The Obama administration is worried that the turmoil in Cairo may stall or derail the political transition in Egypt. It could also hurt Egypt’s already badly battered economy.

“The challenge for the U.S. is how will it continue to support the principles of democracy and engage with Egypt,” said Mr. Shehata.

Mrs. Clinton will arrive in Cairo at a difficult time.

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