The restoration of classified status to more than 55,000 previously declassified pages began in 1999, when the CIA 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, the Times said on its Web site.
The secret program accelerated after the Bush administration took office and especially after the September 11 attacks, according to archives records, the paper said.
It came to light after intelligence historian Matthew Aid noticed dozens of documents he had copied years ago had been withdrawn from the archives' open shelves, the Times said.
Under existing guidelines, government documents are supposed to be declassified after 25 years unless there is a particular reason to keep them secret.
Some historians say the program is removing material that can do no conceivable harm to national security and note that some of the documents have been published by the government, the Times said.
Critics say it is part of a marked trend toward greater secrecy under the Bush administration, which has increased the pace of classifying documents, slowed declassification and discouraged the release of some material under the Freedom of Information Act, the paper said.
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