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WASHINGTON

The National Archives signed a secret agreement in 2001 with the Central Intelligence Agency permitting the spy agency to withdraw from public access records it considered to have been improperly declassified, the head of the archives, Allen Weinstein, disclosed on Monday.

Mr. Weinstein, who began work as archivist of the United States last year, said he learned of the agreement with the C.I.A. on Thursday and was putting a stop to such secret reclassification arrangements, which he described as incompatible with the mission of the archives.

Like a similar 2002 agreement with the Air Force that was made public last week, the C.I.A. arrangement required that archives employees not reveal to researchers why documents they requested were being withheld.

The disclosure of the secret agreements provides at least a partial explanation for the removal since 1999 of more than 55,000 pages of historical documents from access to researchers at the archives. The removal of documents, including many dating to the 1950's, was discovered by a group of historians this year and reported by The New York Times in February.

The reclassification program has drawn protests from many historians and several members of Congress, notably Representative Christopher Shays, the Connecticut Republican who held a hearing on the program last month.

The National Archives, with facilities in College Park, Md., at the presidential libraries and in other locations, are the repository of most official government documents and a major resource for historians.

"Classified agreements are the antithesis of our reason for being," Mr. Weinstein said in a statement. "Our focus is on the preservation of records and ensuring their availability to the American public, while at the same time fulfilling the people's expectation that we will properly safeguard the classified records entrusted to our custody."

In a brief interview, Mr. Weinstein said he was particularly disturbed that the archives had agreed not to tell researchers why documents were unavailable. The C.I.A. agreement said archives employees would "not attribute to C.I.A. any part of the review or the withholding of documents." In the agreement with the Air Force, archives officials said they would "not disclose the true reason for the presence" of Air Force personnel at the archives.

Mr. Weinstein said he would not permit such agreements in the future. If the withdrawal of previously declassified documents becomes necessary, he said, it will be conducted "with transparency," including disclosure of the number of documents removed.

Asked about Mr. Weinstein's statement, Paul Gimigliano, a C.I.A. spokesman, said, "Working very closely over the years with the National Archives, C.I.A.'s goal has been to ensure the greatest possible public access to material that has been properly declassified."

C.I.A. officials have said the reclassification work was necessary because other agencies, including the State Department, released material about intelligence activities without giving the agency a chance to review it.

First Lt. Christy A. Stravolo, an Air Force spokeswoman, said that any decisions on documents that had been "put back into protective custody" complied with federal guidelines. "The Air Force Declassification Office has a very thorough process for review, and there are no shortcuts so as to protect national security," Lieutenant Stravolo said.

Thomas S. Blanton, director of the private National Security Archive at George Washington University, praised Mr. Weinstein's actions.

"He's doing the right thing, no more secret agreements to classify open files," said Mr. Blanton, whose group helped uncover the reclassification program. "The National Archives aided and abetted a covert operation to lie to researchers and white-out history."

Matthew M. Aid, a Washington historian who discovered in December that documents he obtained years ago had been removed from open shelves, said he was "saddened" by the revelation that archives officials had agreed to hide the reclassification program. "I still don't understand why this all had to be done in secret," Mr. Aid said.

John W. Carlin, Mr. Weinstein's predecessor as head of the archives from 1995 to 2005, said in a statement that he knew nothing about the reclassification program and was "shocked" to learn the contents of the secret agreements signed when he was in office.

Michael J. Kurtz, the assistant archivist, who signed both agreements, could not be reached for comment last night. Mr. Weinstein said Mr. Kurtz had told him that he briefed Mr. Carlin about the agreements, but that he understood if Mr. Carlin did not recall being told of the reclassification effort.

Copyright 2006 The New York Times Company