Egypt's Muslim Brotherhood leader Mohammed Badi speaks to the media outside a polling station in Beni Suef on December 15, 2011, during the second round of parliamentary voting. (Mahmud Khaled/AFP/Getty Images)

The dominant showing by the Muslim Brotherhood’s Freedom and Justice Party in Egypt’s first post-revolution elections puts the country on a collision course, analysts say, with emboldened Islamists and the entrenched military set to vie for power.

The Brotherhood, which was the leading opposition force under now-deposed leader Hosni Mubarak, has emerged as the country’s most viable political power. While votes are still being counted in the last of three stages of elections for parliament’s lower house, the Brotherhood expects to take more than 40 percent of seats and could claim an outright majority on Jan. 23, when the new parliament is scheduled to convene.

Until now, the relatively moderate Islamist group had an uneasy alliance with the council of generals who took control of the country after Mubarak’s ouster on Feb. 11. But with the military leaders intent on protecting their political and economic interests as Egypt lurches toward democracy, some analysts say a clash between the two centers of power is inevitable.

The long-term interests of the military leaders and the Brotherhood “do not converge,” said Shadi Hamid, an Egypt expert at the Brookings Doha Center. “The military wants to effectively stay in power behind the scenes. That certainly is not what the Brotherhood wants.”

The powers of the incoming parliament remain unclear and are to be laid out in the as-yet-unwritten constitution, a document that the ruling generals have said they want military-appointed bodies to influence. But the Brotherhood’s Freedom and Justice Party is calling for real powers for the parliament, including the authority to appoint a prime minister and full control over the writing of the constitution.

A shift in U.S. policy

Under Mubarak, the Brotherhood was allowed to exist on a tight leash. Thousands of its members were arrested and tortured. Mubarak also pointed to the organization as the possible alternative to his autocratic rule and used that scenario to scare Western allies, who feared Islamist domination in the region and the unraveling of Egypt’s longtime peace treaty with Israel.

A senior legal adviser to the Freedom and Justice Party has said that elected officials from his party would reassess the $1.3 billion in annual U.S. aid to the Egyptian military.

In an interview on Egyptian television, the adviser, Ahmed Abu Bakar, said U.S. aid to Egypt, including to the military, does not help the economy or Egyptians and would be subject to debate by the new parliament. The statements come at a tense moment in U.S.-Egyptian relations, after security forces stormed the offices of 10 civil society organizations, including three American pro-democracy groups, over accusations of illicit foreign funding.

“Anything that affects Egyptian political decisions and anything that constitutes as intervention in internal Egyptian affairs is something we blatantly refuse,” Bakar said.

In recent months, U.S. diplomats and other officials have met with members of the Freedom and Justice Party. Those meetings mark a shift in policy for the United States, which has long regarded the Brotherhood as a threat to regional stability. But the willingness of Americans to engage the group is a nod to the reality that the Brotherhood will be a decision-maker in Egypt and a major player on the international stage.

As part of a continuum of official U.S. visits, Jeffrey D. Feltman, assistant secretary of state for Near Eastern affairs, arrived in Cairo on Wednesday for talks with military and political leaders.

“We are going to judge these parties not by the names on their doors, the T-shirts they wear, but on their commitment to upholding universal democratic standards” and human rights, including for women and minorities, State Department spokeswoman Victoria Nuland said. “Some of these parties have had quite moderate rhetoric,” she said, “but that rhetoric now has to be matched in the way they proceed.”

Short-term, uneasy alliance

The Egyptian Muslim Brotherhood has inspired Islamist militant movements throughout the region, most notably the Palestinian group Hamas, which the United States and Israel consider a terrorist organization.

Mohamed Beltagy, a leading member of the Brotherhood’s Freedom and Justice Party and a candidate for parliament, agreed with other members of his party that the peace treaty with Israel will be respected, at least during this rocky transitional period. But, he added, “the parliament has the right to revise whatever happened without the public’s consent.”

In the bloody run-up to the elections, which began in November, the Brotherhood faced a storm of criticism from more centrist and liberal revolutionary parties, which alleged that the group was too close to the ruling generals. The Brotherhood’s non-Islamist rivals have accused it of turning a blind eye to Mubarak-style human rights abuses at the hands of the military rulers and betraying the cause of the revolution for seats of power.

Brotherhood spokesman Mahmoud Ghozlan only stoked the tension with a recent proposal to consider granting immunity to military leaders for crimes committed during the transition, which he said would prevent Egypt from further destabilizing. As many as 100 people have been killed in clashes in the past three months; in some cases, brute force was used against unarmed protesters in the capital and other urban centers.

But that reluctance to challenge the military rulers will change, analysts said, noting that the convergence of interest between the Brotherhood and the generals is only short-term.

Analysts say the Brotherhood is waiting to be part of a strong elected body, which the group sees as the only legitimate tool to push the generals out of power and to guarantee its own.

“They are purely political animals,” said Marc Lynch, a Middle East expert at George Washington University. “They think that the only way to unseat the [generals] is to create an alternative institution, a strong parliament with electoral legitimacy.”

Staff writer Karen DeYoung in Washington contributed to this report.