The US State Department says it is "very concerned" about raids by Egyptian soldiers and police on the offices a number of pro-democracy and human rights groups in Cairo.
Activists say 17 groups were targeted and computers and boxes full of files were seized.
Some employees were reportedly prevented from leaving while the searches were held.
The Egyptian news agency Mena said the searchers were part of an investigation into foreign funding and quoted the prosecutor's office as saying there was evidence showing violation of Egyptian laws, including not having permits.
According to the BBC, two of the offices targeted belonged to US -based organisations.
They are the National Democratic Institute (NDI) and the International Republican Institute (IRI), which are loosely associated with the US Democratic and Republican parties respectively.
A State Department spokesperson in Washington said the Egyptian authorities needed to stop the "harassment" of NGO staff, return all property and "resolve this issue promptly".
She said it was inconsistent with the bilateral co-operation Egypt and the US had had over many years.
Analysts say the authorities are concerned the organisations may be refuelling the recent resurgence in protests.