Washington says it is "deeply concerned" over reports that Egypt plans to move ahead with plans to put on trial more than 40 employees of U.S.-funded NGOs.
State Department spokeswoman Victoria Nuland said U.S. officials were seeking clarification from their Egyptian counterparts.
Egypt's military rulers have accused 43 people, including 19 Americans, of using foreign funds to foment unrest in their country.
The accused are not allowed to leave Egypt.
As part of the probe, heavily armed Egyptian security forces raided the offices of 17 pro-democracy and rights groups in December.
U.S. Secretary of State Hillary Clinton has warned Egypt that it could lose $1.5 billion in U.S. aid earmarked for this year if it fails to resolve the dispute.
Responding to Clinton's remark, Egyptian Foreign Minister Muhammad Amr said the government cannot interfere in the work of the judiciary.
Another Egyptian official, International Cooperation Minister Aboul Naga, said she would pursue the case through to the end. Naga, whom some observers describe as a holdover from the regime of Hosni Mubarak, said the probe into the NGOs had uncovered "plots aimed at striking at Egypt's stability."
According to Egyptian security officials, among those reportedly being held is Sam LaHood, head of the Egyptian office of the U.S.-funded International Republican Institute (IRI) and son of U.S. Transportation Secretary Ray LaHood.
In a statement, the IRI called the case "politically motivated" and carried out "in part by Mubarak-era holdovers."
Some critics say Egypt's military rulers are using the case to deflect criticism from liberals and secular groups who fault the generals for moving slowing on transitioning to democracy.
The military often claims "foreign hands" are behind the protests to their rule, and accuse protesters of being funded from abroad in a bid to destabilize the country.
Egypt has been rocked by a fresh wave of protests sparked by the deaths of 74 fans at a soccer game amid accusations security forces did little to prevent the bloodshed.
Compiled from agency reports