The United States demanded "clarification" over Cairo's apparent plans to put dozens of pro-democracy activists, including 19 Americans, on trial over charges of illegal funding of aid groups.
US State Department spokeswoman Victoria Nuland said Washington was "deeply concerned" over the developments, which threatened to further strain ties with Egypt's post-Arab Spring military rulers.
A top official at Freedom House, one of the groups targeted, called Egypt's handling of the matter "a disaster."
A judicial source in Cairo told AFP 44 people, including Egyptians, would be tried over alleged illegal funding of aid groups, a day after the United States said it would review aid to Egypt, $1.3 billion last year, over the crackdown.
"We have seen media reports that judicial officials in Egypt intend to forward a number of cases involving US-funded NGOs to the Cairo criminal court," Nuland told reporters traveling with Secretary of State Hillary Clinton.
"We are deeply concerned by these reports and are seeking clarification from the government of Egypt."
The offices of Freedom House and the International Republican Institute were among 17 local and international NGOs raided in December by Egyptian authorities as part of a probe into alleged illegal funding.
The aid workers are accused of "setting up branches of international organizations in Egypt without a license from the Egyptian government" and of "receiving illegal foreign funding."
A travel ban on all the NGO workers who were detained remains in place.
The decision to try the foreign workers comes as Egypt remains beset by unrest sparked by the perceived failure of its military rulers and police to prevent football-linked violence following a match in the northern city of Port Said on Wednesday that left 74 people dead.
The decision to forward the NGO workers' cases for trial drew condemnation from US groups with staff in Egypt and from Germany's government.
"The Egyptian military's handling of this issue has been a disaster," said Charles Dunne, director for Middle East and North Africa programs for Freedom House.
"This represents another escalation by the Egyptian government in its war on civil society -- and it's not just the US organizations, it's the Egyptian organizations," he told AFP.
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"I find it astounding that they would do this while you still have a delegation of Egyptian general officers here in the United States to talk to the Congress and the administration about continued US military funding."
German Foreign Minister Guido Westerwelle slammed Egypt's decision.
"It is unacceptable to harm organizations that have a real international mission which they take on seriously," he told ARD television, according to an early release transcript.
"We shall act, in the framework of our foreign policy towards Egypt, in such a way as to ensure that political organizations that have a worldwide reputation are allowed to continue working as they have done."
Egypt's ruling military council, which took power after an uprising toppled veteran president Hosni Mubarak last spring, has accused foreign groups of funding street protests against them.
The move will further strain US-Egypt ties after last year's raid during which Cairo prosecutors confiscated computers and paperwork from NGO offices.
Egypt then barred some US members of the NGOs from leaving the country and American officials said "a handful" took refuge inside the US embassy.
On Saturday, Clinton warned that Washington's aid to Egypt would be reviewed, highlighting the continued deadlock over Cairo's crackdown.
In a meeting with Egyptian Foreign Minister Mohamed Amr on the sidelines of the Munich Security Conference, Clinton said she "had a chance to once again express our deep concerns with what is happening to our NGOs."
"We do not believe there is any basis for these investigations, these raids... the seizure of their equipment and certainly no basis for prohibiting the exit from the country by" NGO members," Clinton said.
"We have worked very hard the last year to put into place financial assistance and other support for the economic and political reforms that are occurring in Egypt.
"And we will have to closely review these matters as it comes time for us to certify whether or not any of these funds from our government can be made available under these circumstances," Clinton added.
Senior Egyptian military officers visited the United States last week in a bid to defuse the row.
Among those barred from leaving the country is the Egypt director of IRI, Sam LaHood, the son of US Secretary for Transportation Ray LaHood.