The Federal Bureau of Investigation has collected at least 3,500 pages of internal documents in the last several years on a handful of civil rights and antiwar protest groups in what the groups charge is an attempt to stifle political opposition to the Bush administration.

The F.B.I. has in its files 1,173 pages of internal documents on the American Civil Liberties Union, the leading critic of the Bush administration's antiterrorism policies, and 2,383 pages on Greenpeace, an environmental group that has led acts of civil disobedience in protest over the administration's policies, the Justice Department disclosed in a court filing this month in a federal court in Washington.

The filing came as part of a lawsuit under the Freedom of Information Act brought by the A.C.L.U. and other groups that maintain that the F.B.I. has engaged in a pattern of political surveillance against critics of the Bush administration. A smaller batch of documents already turned over by the government sheds light on the interest of F.B.I. counterterrorism officials in protests surrounding the Iraq war and last year's Republican National Convention.

F.B.I. and Justice Department officials declined to say what was in the A.C.L.U. and Greenpeace files, citing the pending lawsuit. But they stressed that as a matter of both policy and practice, they have not sought to monitor the political activities of any activist groups and that any intelligence-gathering activities related to political protests are intended to prevent disruptive and criminal activity at demonstrations, not to quell free speech. They said there might be an innocuous explanation for the large volume of files on the A.C.L.U. and Greenpeace, like preserving requests from or complaints about the groups in agency files.