Secretary of State Hillary Clinton met with Field Marshall Mohamed Hussein Tantawi today, after meeting Egypt’s newly elected president Mohamed Morsi yesterday on her first visit since the uprising that ousted long-time US ally Hosni Mubarak.

Ms. Clinton’s trip illustrates the balancing act the US is playing in Egypt, where Mr. Morsi, a member of an Islamist group long held in suspicion by US policymakers, and the military, recipient of billions of dollars in aid from Washington, are locked in a power struggle.

In brief remarks after her hour-long meeting with Morsi yesterday, Clinton said the US “supports the full transition to civilian rule with all that entails,” and that she is “working to support the military’s return to a purely national security role.” But she also praised the military for holding free and fair elections, and for not firing on Egyptians during the uprising against Mubarak, comparing the Egyptian uprising to Syria, where “the military [is] murdering their own people.”

The Supreme Council of the Armed Forces (SCAF), the military council that ruled Egypt after Mubarak’s fall, made a last-minute power grab before handing over executive authority to Morsi, the candidate of the Muslim Brotherhood movement, at the end of last month. After a court seen as aligned with the generals ruled that Egypt’s newly-elected parliament should be dissolved, the generals issued amendments to Egypt’s interim constitution that limited the president’s powers and extended its own, breaking its promises of completing a full transition to civilian rule by this month.

In his first week in office, Morsi shot back, ordering the parliament to reconvene despite the court’s ruling. He backed off after the court affirmed its first ruling, and said he would respect the law. This week, a court is due to rule on a case that could dissolve the constitutional assembly elected by the Muslim Brotherhood-dominated parliament, which would give the generals a chance to unilaterally appoint a new body to write Egypt’s new constitution.

Despite the $1.3 billion in US aid to the military every year, the US has found over the last year that it had little leverage over the generals. While Clinton talked about ending the political role of the military yesterday, she indicated the US would not interject in the power struggle.

 “…There is more work ahead, and I think the issues around the parliament, the constitution have to be resolved between and among Egyptians,” she said, adding that such issues are not uncommon in transitions away from military-dominated rule.

Clinton is the highest US official yet to meet with Morsi. Before Mubarak’s ouster, US officials rarely met with Brotherhood members, meeting only those who were elected members of parliament in their capacity as lawmakers. But Clinton stressed the “broad” and “enduring” nature of the US relationship with Egypt, which has been a key ally in the Middle East, particularly in keeping peace with Israel.

But Clinton’s attempts to build a relationship with Morsi that will carry forward the US-Egypt partnership have spurred anger from some Egyptians who say the US is supporting the Muslim Brotherhood and helping it to dominate all branches of Egypt’s government. Protesters outside her hotel and outside the presidential palace where she met with Morsi rejected her visit yesterday.

“We are seeing the American policy is biased toward the Islamists in its confrontations with the SCAF,” says Emad Gad, an analyst at the Al Ahram Center for Political and Strategic Studies, and a former member of parliament with the Egyptian Social Democratic Party, which has often been at odds with the Brotherhood’s party. “We want to see some sort of balance between our institutions. Morsi is getting support from the US in order to isolate the SCAF and gain control over the legislative and executive powers in Egypt.”

Those who take this view cite as proof US warnings urging the military to pass power to elected civilians, including during the week between the election and the announcement of the winner when it appeared Morsi had won but the announcement was delayed. The fact that Morsi’s statement reconvening the parliament was issued just hours after his meeting with visiting US Deputy Secretary of State William Burns deepened their perceptions. US officials say they simply want the military to pass power to those elected in free and fair elections.

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