CAIRO—As Muslim Brotherhood leader Mohammed Morsi prepares to become Egypt´s first freely elected president on Saturday, his unlikely rise has upended Egyptians´ perceptions of America´s place in their domestic politics.

The regime of former President Hosni Mubarak received strong support from the U.S. government for decades, and his military received $1.3 billion of U.S. aid each year. The Muslim Brotherhood viewed the U.S. with suspicion, and the U.S. long reciprocated by limiting its interactions with the then-banned organization.

These days, though, some jilted supporters of former regime stalwart Ahmed Shafiq, who lost to Mr. Morsi in the election, are peddling the accusation that U.S. officials backed the Muslim Brotherhood´s candidate, an assertion denied by the U.S. government, which insists it supported only a fair and transparent election process.

The Brotherhood, meanwhile, has publicly warmed up to the superpower that for decades looked on it with deep concern.

U.S. policy makers and Egyptian politicians say they can´t predict how the changing perceptions of the U.S. will play out. But the abrupt change—with Islamists courting U.S. favor while military and old-regime loyalists assail their erstwhile U.S. backers—offers a rare opportunity for U.S. diplomats to recalibrate their relationship with Egypt.

"Things are definitely, definitely in play," said Elijah Zarwan, a senior fellow at the London-based European Council on Foreign Relations. "The Brotherhood and the military will be, after July 1, kind of roommates in the presidential palace, if you will. I think U.S. policy has to find a way to support them both."

For the time being, emotions among some liberals and supporters of the military and the former regime are raw. Before official election results were announced on Sunday, several politicians from liberal and leftist parties held a news conference to denounce the Brotherhood and, in the next breath, accused the U.S. of interfering in Egypt´s internal affairs.

They pointed to comments by U.S. officials that they said showed new U.S. support for the Brotherhood. Secretary of State Hillary Clinton, for example, after unofficial election results suggested Mr. Morsi had won, urged Egypt´s military rulers to "turn over power to the legitimate winner."

To some secularists and former regime officials, the U.S. messages sounded like endorsements of the Brotherhood.

"Now we see the U.S. encouraging the military to hand over power in Egypt to the Muslim Brotherhood," said Osama Al Ghazali Harb, a former member of Egypt´s U.S.-backed former ruling party and now the head of the secular-minded Democratic Front Party. "We refuse that the Muslim Brotherhood should come to power leaning on American support."

U.S. officials say they didn´t take sides. "There was a perception among many groups who supported Shafiq that we actively backed Morsi," said a U.S. Embassy official in Cairo. "It´s wrong. We didn´t. We supported a process."

Relations between the U.S. and the Brotherhood, however, have improved dramatically since the uprising against Mr. Mubarak in early 2011.

During the past 16 months, the Brotherhood has sent dozens of goodwill delegations to meet with officials in Washington to assure policy makers of their commitment to democracy, economic liberalism and civil rights. State Department officials and some prominent American lawmakers have held meetings with senior Brotherhood leaders in Cairo.

While many secular-minded politicians only met with U.S. officials in secret, the Brotherhood trumpeted their meetings in media reports.

Meanwhile, the Egyptian military and U.S. have tested the limits of each other´s patience, and Egypt´s ruling generals have spent much of the past year publicly accusing the U.S. of meddling in its internal affairs in order to undermine its shift toward democracy.

In the most notable case last winter, the son of American cabinet secretary and six other American non-governmental employees were barred from leaving Egypt and charged with violating a highly restrictive law on foreign funding for civil society groups. A judge eventually allowed the Americans to return home, but not before military-appointed cabinet officials publicly accused them of stoking unrest in the service of nebulous political ends.

As the NGO episode brought Washington dangerously close to breaking off its relationship with the Egyptian military, the Brotherhood quietly reassured U.S. officials that it wanted to see the NGO law revised to allow American organizations to work freely.

Allegations the U.S. played favorite in the election come against the background of a potentially bruising fight between Mr. Morsi and the military, which has ruled over the democratic transition and taken steps to maintain significant powers over policy.

The next few days could give an indication of Mr. Morsi´s willingness to compromise with military leaders. An Egyptian state media report on Thursday said the president-elect would take the oath of office on Saturday in front of the same Supreme Constitutional Court that moved to dissolve the elected, Muslim Brotherhood-dominated parliament two weeks ago. Mr. Morsi´s campaign had pledged to take the oath of office in front of the dissolved assembly.

Yet another state media report said Mr. Morsi would deliver a speech at a protest Friday demanding that the military reinstate the dissolved parliament and withdraw a constitutional declaration that limits presidential powers.

The military, meanwhile, promoted the view that Mr. Morsi would be conciliatory. Maj.-Gen. Mohamed Assar, a member of the ruling Supreme Council of armed Forces, said in a televised statement on Wednesday evening that Mr. Morsi would keep Field Marshal Hussein Tantawi, Egypt´s acting president, as minister of defense.

Representatives of Mr. Morsi couldn´t be reached to confirm the statement or media reports.

Write to Matt Bradley at matt.bradley@dowjones.com (Copyright © Dow Jones & Company, Inc.) 06/29/12)