The state archives, which is a division of the State Education Department and is not controlled by the governor, has provided inaccurate information about the contents of its holdings. In late June, the archives told The New York Times, in writing, that it had no documents from Mr. Cuomo related to the inquiry. The document was a response to a Freedom of Information Law request; the archives and the governor’s office now acknowledge that the response was incorrect, but say it was issued in error.

In the course of defending its handling of archived documents, the administration has criticized The Times Union. In a letter to the paper, Mr. Cuomo’s communications director, Richard Bamberger, said The Times Union was working on a “manufactured story” and was trying to “create controversy.” Mr. Bamberger accused the paper of trying to atone for its role in the history of the trooper inquiry; in 2007, an article published in the paper set off the controversy, and some suggested that the paper had been used by Mr. Spitzer for political purposes.

“We are aware of your efforts to generate doubt about the validity of the Troopergate report, which was embarrassing to The Times Union,” Mr. Bamberger’s letter said, adding, “But it would be shameful for you to compound your prior errors by making use of your news pages to try to rehabilitate your own image by manufacturing doubt about professional work done by career prosecutors in the public interest.”

The Cuomo administration has seemed particularly concerned about a memorandum written by Ms. Lacewell, summarizing the investigation after it was over. The Times Union obtained a copy of the memorandum before Mr. Cuomo’s aides removed it from public view; the administration said it was a protected document because it was a “work product,” and The Times Union has not published it.

Rex Smith, the editor of The Times Union, said, “Our goal first was to do a story about what we thought was a significant departure from traditional practice in terms of access to documents in the archives.” He said the paper was still weighing whether to do an article about the memo.

On Monday, state officials struggled to explain why The Times was misled by the archives about the presence of records on the inquiry. Dennis Tompkins, a spokesman for the archives, said officials at first thought they did not have any records related to the matter, because no records were labeled as such.