A member of the Muslim Brotherhood greets another parliament member during the first day of the new session in January. The Muslim Brotherhood’s growing influence has been growing since then. (Asmaa Waguih/Reuters)

As Egypt’s ruling generals near the end of their formal reign, the country’s main Islamist party is asserting increasing authority over the political system and openly confronting the powerful military.

The Muslim Brotherhood’s growing influence came into sharp focus Sunday as its political wing and other Islamists established a dominant role in the 100-member body chosen by the parliament to write the country’s new, post-revolutionary constitution. Liberals and leftists vowed to boycott the assembly, and at least eight withdrew from it, accusing the Islamist parties of taking over the process.

The move came just days after the Brotherhood said it was considering putting forth a presidential candidate from its ranks, something it had promised not to do.

The rift between the once-underground group and the military burst into the open this weekend, with the Brotherhood issuing a scathing statement calling the military-appointed government a failure and raising concern over the credibility of the upcoming presidential election. The military council fired back Sunday, condemning the Brotherhood for “doubting” the institution and making “fabricated” allegations.

The Brotherhood and its political wing, the Freedom and Justice Party, were initially hesitant to challenge the military after the revolt that ousted President Hosni Mubarak last year. But the Islamist movement became emboldened after winning nearly half the seats in parliament in elections that ended in February.

Now, its leaders are going so far as to oppose the generals’ private requests for immunity from prosecution for accusations of killings and mistakes committed during Egypt’s political transition, something they were open to just two months ago. They are demanding the dissolution of the military-appointed government of Prime Minister Kamal el-Ganzouri.

Some in the Brotherhood leadership are even ready to go after the military’s economic holdings. Brotherhood members are calling for various military industries, estimated at 5 to 45 percent of the nation’s economy, to be placed under parliamentary oversight and added to the national treasury. The military has fiercely resisted that prospect.

“There’s been a major shift in Egyptian politics,” said Shadi Hamid, an expert on the Brotherhood at the Brookings Institution’s Doha Center. “The Supreme Council of the Armed Forces is entering its lame-duck stage. At this point, no one can stop the Brotherhood.”

The aged and increasingly unpopular generals are still in control of Egypt, a longtime U.S. ally considered a linchpin for Middle East peace. But the Brotherhood has been able to leverage its influence using the parliament, which is likely to become a key vehicle for channeling popular concerns, analysts said. Already, the military council has been forced to cave on several key issues amid public discontent.

Some analysts said the growing confrontation might endanger the political transition, with presidential elections less than two months away.

The Brotherhood, however, appears emboldened and ready to challenge the military. As the group consolidates power, it is increasingly willing to take up issues popular with its constituents but anathema to the ruling generals, said Marc Lynch, director of the Institute of Middle East Studies at George Washington University.

That includes questioning the continued acceptance of around $1.5 billion in U.S. aid, which mainly goes to the military. Although that money has helped forge a strong bond between Washington and Cairo, many Egyptians see it as a payoff for Egypt’s subservience.

Lynch said, however, that he expects the Brotherhood will stop short of outright confrontation and will instead try to maneuver the generals aside as quickly as possible without destabilizing Egypt.

Brotherhood leaders have portrayed themselves as pragmatists who will maintain the country’s peace treaty with Israel and focus on the country’s unemployment and poverty rather than social issues such as banning alcohol.

The Brotherhood’s more assertive stance has come after months of maneuvering through the murky military-led transition that followed Mubarak’s fall. Critics of the Brotherhood have accused the Islamist group of cutting backroom deals with military rulers to secure the organization’s rise to power and remaining quiet about military missteps and abuses when others protested.

“The Brotherhood is searching for power, and the military council is looking for a safe ticket out,” said Ibrahim Mohyeldin, a member of parliament from the liberal Free Egyptians party. “They have a deal.”

The Islamists have denied any such pact.

In the Brotherhood’s new headquarters in suburban Cairo, top officials made it clear that they now agree on little with the military council — the Supreme Council of the Armed Forces, or SCAF — other than the plan to transition to an elected president by the end of June. But they also remain cautious.

“We don’t have a honeymoon relationship with SCAF, as some people think, and we don’t have a tough relationship with them, either,” Mahmoud Hussein, the secretary general of the Brotherhood, said in a recent interview. “We praise them when they do something good, and we criticize them when they do something bad.”

But the criticisms are mounting. Mahmoud Ghozlan, the Brotherhood spokesman who just two months ago advocated immunity for the generals, said the group changed its position when it became clear the Egyptian people had rejected the idea. Ghozlan and Hussein signaled that the group intended to go after the generals’ previously sacred military production budget.

“When there are [military-owned] companies for water bottling, agricultural companies, petrol stations, food products, why should all those stay a secret?” Ghozlan said.

Liberals and leftists worry that the Brotherhood and other Islamist groups will leave them marginalized. They point to the Brotherhood’s huge role in the constitutional assembly, which will draft a document that will map out the role of religion, the executive and parliamentary powers and minority rights in the new Egypt.

“We are going to boycott this committee, and we are going to withdraw and let them make an Islamic constitution. We are going to continue struggling for a secular Egypt in the streets,” said Mohammed Abou el-Ghar, head of the Social Democratic Party, who was elected to the assembly but has resigned his post.

He noted that Brotherhood officials had said initially the committee would represent all Egyptians’ views. “But as you can see, there is no representation of secular Egypt,” he said.

The Brotherhood’s political wing denied the accusations on Sunday, calling the assembly diverse and representative.

At least 60 percent of the 100 assembly members are Islamists or have Islamist backgrounds. That reflects the role played by the parliament — where Islamists were elected to more than 70 percent of the seats — in choosing the members.

Inside the parliament building, Sobhi Saleh, a leading member of the Brotherhood’s political wing, walks with an unmistakable swagger. In a recent interview, he said the liberals and secularists who worry the Islamist ascendancy will cut them out should face the facts and work with the Brotherhood.

“After the revolution, the Brotherhood became a reality that no one can ignore,” he said.

Special correspondent Ingy Hasseib contributed to this report.