In a seven-year-old secret program at the National Archives, intelligence agencies have been removing from public access thousands of historical documents that were available for years, including some already published by the State Department and others photocopied years ago by private historians.

The restoration of classified status to more than 55,000 previously declassified pages began in 1999, when the Central Intelligence Agency and five other agencies objected to what they saw as a hasty release of sensitive information after a 1995 declassification order signed by President Bill Clinton. It accelerated after the Bush administration took office and especially after the 2001 terrorist attacks, according to archives records.

But because the reclassification program is itself shrouded in secrecy — governed by a still-classified memorandum that prohibits the National Archives even from saying which agencies are involved — it continued virtually without outside notice until December. That was when an intelligence historian, Matthew M. Aid, noticed that dozens of documents he had copied years ago had been withdrawn from the archives' open shelves.

Mr. Aid was struck by what seemed to him the innocuous contents of the documents — mostly decades-old State Department reports from the Korean War and the early cold war. He found that eight reclassified documents had been previously published in the State Department's history series, "Foreign Relations of the United States."

"The stuff they pulled should never have been removed," he said. "Some of it is mundane, and some of it is outright ridiculous."

After Mr. Aid and other historians complained, the archives' Information Security Oversight Office, which oversees government classification, began an audit of the reclassification program, said J. William Leonard, director of the office.

Mr. Leonard said he ordered the audit after reviewing 16 withdrawn documents and concluding that none should be secret.

"If those sample records were removed because somebody thought they were classified, I'm shocked and disappointed," Mr. Leonard said in an interview. "It just boggles the mind."