At least 17 US-based and local groups receiving foreign funding were targeted, according to activists and Egyptian state media.
An official said at least one of the US-based groups was operating without proper permits.
The US state department said it was "very concerned" and urged authorities to stop the "harassment" of NGO staff.
Some civil society activists have reported that employees were prevented from leaving while searches continued.
"This is not appropriate in the current environment," state department spokeswoman Victoria Nuland said, adding that senior US officials had been in touch with Egyptian military leaders to express their concern over the raids.
Egypt's military has vowed to investigate how pro-democracy and human rights organisations are funded and has said repeatedly it will not tolerate foreign interference in the country's affairs.
"The public prosecutor has searched 17 civil society organisations, local and foreign, as part of the foreign funding case," official news agency Mena cited the prosecutor's office as saying.
"The search is based on evidence showing violation of Egyptian laws including not having permits."
The US-based groups targeted include the National Democratic Institute (NDI) and the International Republican Institute (IRI), loosely associated with the US Democratic and Republican parties.
'Guardians of freedom'
Documents and computers have been seized as part of the investigations and one report said that the IRI's doors had been sealed with wax.
Julie Hughes, Cairo Director of the NDI, told the BBC about 14 members of the security forces had turned up at its offices.
"They came in and asked all of us to gather together in a room, to leave the laptops on our desks, and open and accessible," she said.
"They went around the room from computer to computer looking through files and then gathering up those computers, and then about four and a half hours later they left."
Both pro-democracy groups, who say they take a neutral political stance, run programmes to train members of nascent political parties in democratic processes.
The Arab Centre for the Independence of Justice was also among those being investigated, its head, Nasser Amin, told AFP.
Civil society groups have responded angrily to the raids.
"[Former President Hosni] Mubarak's regime did not dare to undertake such practices prior to the uprising," the Arabic Network for Human Rights Information said in a statement.
The group said the authorities were "aiming to intimidate activists and rights advocates, gag their mouths and freeze their activities in support of human rights and against repression and torture".
Nobel peace laureate and Egyptian reformist Mohamed ElBaradei said any attempt to stifle such groups would surely backfire.
"Human rights organisations are the guardians of nascent freedom. Efforts to suffocate them will be a major setback," he wrote on his Twitter account.
Egyptian soldiers and police have raided the offices of non-governmental organisations (NGOs) in Cairo.