WASHINGTON — The Obama administration plans to resume military aid to Egypt, American officials said on Thursday, signaling its willingness to remain deeply engaged with the generals now running the country despite concerns over abuses and a still-uncertain transition to democracy.

To restart the aid, which has been a cornerstone of American relations with Egypt for more than three decades, the administration plans on sidestepping a new Congressional requirement that for the first time directly links military assistance to the protection of basic freedoms.

Secretary of State Hillary Rodham Clinton is expected to waive the requirement on national security grounds as soon as early next week, according to administration and Congressional officials. That would allow some, but not yet all of $1.3 billion in military aid this year to move forward, said the officials, who spoke on the condition of anonymity so that they could discuss internal deliberations.

The threat that the military aid might end was a critical factor in the release by the Egyptian government of seven Americans employed by four American-financed international organizations that were involved in community organizing activities. The prosecutions of the Americans were part of broader concerns the Obama administration has had about Egypt’s progress since the overthrow of Hosni Mubarak a year ago.

The outcome is not likely to please either human rights advocates concerned about abuses by Egypt’s security forces or many Egyptians, who have grown disillusioned with the military council and hostile toward American interference in Egyptian affairs. At a time of rising anti-American sentiment, the waiver may also alienate the revolutionaries and political reformers struggling to push the country toward civilian rule.

“Making such a certification would undermine the brave struggle of the Egyptian people for a society founded on respect for human rights and the rule of law,” Adotei Akwei of Amnesty International USA wrote in a letter to Mrs. Clinton released on Thursday. “Waiving the certification requirement would forfeit a key form of pressure for the advancement of human rights.”

The State Department’s spokeswoman, Victoria Nuland, said a final decision had not yet been made over resuming the aid, but other officials said there was still a question over how to write the waiver.

President Obama, Mrs. Clinton and other senior officials explicitly warned Egypt’s military leaders that the aid this year was at risk because of the prosecution of the American-financed organizations, which include Freedom House, the International Republican Institute and the National Democratic Institute. The case, which began in December, continues, though Egyptian authorities, under intense pressure from the administration, lifted a travel ban on the seven American employees of the groups. The individuals were allowed to depart after the groups paid nearly $4 million in bail.

One administration official said that with the prosecution still under way, it was impossible for Mrs. Clinton to certify Egypt under the new law, which says that its leaders must carry out “policies to protect freedom of expression, association and religion, and due process of law.” At the same time, Egypt has seated a new Parliament in elections widely seen as free and fair, and it has scheduled a presidential election in May, with a runoff to follow in June. In addition, officials said they believed the aid was crucial to maintain close cooperation with Egypt’s military on regional security and counterterrorism.

Besides the military assistance, the United States has budgeted $250 million for economic and political programs, including those targeted by the Egyptian courts. It has also proposed continuing military aid next year and creating a new $770 million fund to support economic development across North Africa.

Only the military assistance is tied to the certification on basic freedoms, though all assistance to Egypt requires the State Department to certify that the country continues to honor the Camp David peace treaties with Israel. The administration succeeded in including the waiver authority in the new law, giving Mrs. Clinton flexibility to allow some aid, without a blanket waiver.

Within the administration, some officials have argued that the certification should wait until the presidential election, but Egypt’s military has exhausted previously authorized aid and has received no new American funds since the current fiscal year began in October.

Within weeks Egypt risks missing payments on defense contracts, largely with American arms manufacturers, forcing Mrs. Clinton to decide the certification question now. “It’s coming up sooner than some people wanted,” one senior official said.

The pressure the administration put on Egyptian authorities to resolve the fate of the Americans working for nongovernment organizations provoked an angry reaction in Cairo. After the Americans were released and six of them left the country, the new Parliament, in a symbolic action, debated rejecting American aid outright, and questioned relations with Israel.

In Washington, such moves have heightened concerns, especially among lawmakers who imposed the conditions on aid. “The Parliament has said some things that are very chilling,” Senator Lindsey Graham, Republican of South Carolina, said at a budget hearing this week. “We’re not going to throw good money after bad,” he added.

Many in Congress, though, share the administration’s wariness off cutting off assistance altogether. “The strength of Egypt, its stability, is important to the region and to the world,” the House Democratic leader, Nancy Pelosi, said on Thursday during a visit to Cairo with a delegation of lawmakers, “and we want to be helpful in that regard.”

But Tom Malinowski, director of the Washington office of Human Rights Watch, said the administration needed to rethink assistance to Egypt after decades of focusing it largely on the military.

“There’s a much bigger question here,” he said, “and that is: if we want to help a post-Mubarak Egypt, does the current aid package make the slightest bit of sense?” (Copyright 2012 The New York Times Company 03/16/12)