A senior U.S. senator warned the State Department on Friday against disbursing any of this year’s $1.3 billion in military aid to Egypt until its armed forces leadership makes a clear commitment to ongoing democratic transition.

“I would not want to see the U.S. government write checks for contracts with Egypt’s military under present uncertain circumstances,” Sen. Patrick J. Leahy (D-Vt.) said in a statement.

Leahy, who heads the appropriations subcommittee in charge of foreign assistance, wrote restrictions on military aid to Egypt that Secretary of State Hillary Rodham Clinton waived in March on national security grounds.

Egypt’s generals formally closed the doors of a newly constituted parliament on Friday following a determination by the country’s Supreme Constitutional Court a day earlier that some legislators were elected illegally. The move threw into question this weekend’s final round of the presidential election to replace the ruling military council.

The fast-moving events have left the Obama administration frustrated and largely sidelined, and it was not clear that either disbursing or withholding aid would have any effect on the situation.

“To call the Americans bystanders in Egypt would be too strong a word, but it gets you in the right direction,” said a senior U.S. intelligence official who spoke on condition of anonymity because of the sensitivity of the situation. “Absent intervention, U.S. ability to effect change is limited. We’re stuck on the sidelines.”

The administration supported last year’s supposedly temporary takeover by Egypt’s powerful military as a means of replacing ousted president Hosni Mubarak while ensuring a smooth transition to democracy. Since then, the United States has seen its influence with the generals wane through a series of crises in the once-strong relationship.

Leahy added restrictions on foreign military financing — the State Department aid program that provides money for other countries to buy U.S. military equipment — to the most recent appropriations bill. He urged Clinton to implement the restrictions in March after the military council shut down U.S-funded nongovernmental organizations and delayed in lifting emergency laws.

Clinton decided instead to use the law’s waiver provisions on the grounds that U.S. security interests would be harmed, along with U.S. defense contractors, if assistance were stopped.

In elections for the recently seated parliament, secular politicians favored by the administration were overwhelmed by the Muslim Brotherhood, which won nearly half of the seats. The presidential election pits Mohamed Morsi, the Brotherhood candidate, against Ahmed Shafiq, Mubarak’s last appointed prime minister and the military’s favored candidate.

The administration’s conundrum is that it shares many of the military’s concerns about the direction of Egyptian politics, even as it supports free and fair elections and the military’s promise to return to the barracks next month.

Leahy made clear where his own sentiments lie.

Thursday’s court decision “obviously throws into question the future of the transition,” he said in a statement. “Parliament has been dissolved and the military has reaffirmed martial law and has assumed whatever authority the parliament had. There is also the question of whether the victor of the presidential runoff will be allowed to actually assume the authority of the office.”

In comments before Leahy’s statement, State Department spokeswoman Victoria Nuland declined Friday to take a stand on the actions of either the military or Egypt’s Supreme Court, saying that the administration was “continuing to monitor the situation.”

“We’re looking closely at the decisions that were made yesterday and their full implications,” Nuland said. “Our sense of this is it’s not exactly clear to Egyptians themselves what the path forward is. But if in fact the conclusion is that there need to be new parliamentary elections, our hope is that they could happen swiftly and that they reflect the will of the Egyptian people.”

More immediately, she said, “we are hoping and expecting that [presidential elections] will be free, fair, transparent.” The military council “has pledged to step down, turn over power to the elected leader on July 1, and we expect them to meet that commitment.”