At a news conference, the two investigating judges described the non-governmental organizations as political, The New York Times reported. They include the National Democratic Institute and the International Republican Institute, which have financial backing from the U.S. government and are charged with promoting democracy.
Egypt says 19 U.S. citizens were among the 43 people involved in illicit activities. Only five are in the country, including Sam LaHood, the son of Transportation Secretary Raymond LaHood.
Congress and the Obama administration have pressured Egypt to drop the prosecution, with threats of an aid cutoff. But Prime Minister Kamal el-Ganzouri said the investigation will continue.
"Egypt will not yield," he said.
Anyone convicted could receive five-year prison sentences. LaHood and the other Americans are being sheltered in the U.S. Embassy in Cairo.