One of them is the son of U.S. Transportation Secretary Ray LaHood. Egypt charges that the groups fund and support anti-government protests. The groups deny that.
For a fifth day, clashes between protesters and security forces continued. Protesters could be seen pelting rocks at police, who responded by firing back tear gas.
The latest violence is in response to the inability of authorities to prevent a riot after a soccer match, which left 74 people dead.
Washington has reacted angrily to the case, which started with raids last month on the offices of the groups. U.S. Secretary of State Hillary Rodham Clinton has warned it could jeopardize U.S. aid to Egypt, which amounts to more than $1 billion a year.
The Egyptian investigation into the work of the nonprofit groups is closely linked to the political turmoil that has engulfed the nation since the ouster a year ago of President Hosni Mubarak, a U.S. ally who ruled Egypt for nearly 30 years.
The Associated Press contributed to this report.