The White House failed to archive some e-mails in accordance with normal procedures in 2003, according to a letter from a special prosecutor investigating the leak of a CIA operative’s identity.

The prosecutor, Patrick Fitzgerald, disclosed the failure last week to defense attorneys for a former White House official, I. Lewis Libby, who is facing perjury and obstruction of justice charges in the probe.

“We advise you that we have learned that not all e-mail of the Office of Vice President and the Executive Office of the President for certain time periods in 2003 was preserved through the normal archiving process on the White House computer system,” Mr. Fitzgerald wrote in the January 23 letter, which was filed in federal court on Tuesday.

A White House spokesman, Kenneth Lisaius, said yesterday he could not comment on matters under investigation by the special counsel.

A spokesman for Mr. Fitzgerald, Randall Samborn, also declined to comment. The letter does not indicate how thoroughly prosecutors explored the issue of the missing e-mails. However, Mr. Fitzgerald wrote that he did not believe any evidence disappeared that was relevant to the charges against Mr. Libby.

The preservation of the White House’s e-mail files has been an issue of legal contention since the 1980s, when the Reagan White House sought to dispose of records from an early electronic messaging system. A court blocked the destruction.

“It seems pretty surprising that there would be a failure to preserve records when this issue was litigated in the 1980s and 90s,” an attorney for a non-profit group that gathers declassified government records, the National Security Archive, Meredith Fuchs, told The New York Sun. “It’s particularly surprising given that there are investigations going on about things that could have happened within the Office of the Vice President or the Office of the President.”

The missing e-mails could be relevant to a series of ongoing inquiries, including the criminal probe into influence peddling by a lobbyist, Jack Abramoff.

“Entities are under an obligation to preserve their emails if there is an anticipation of litigation,” Ms. Fuchs said.

In 2000, the Clinton White House became embroiled in debate over a failure to preserve some of its e-mails. The Justice Department investigated and a House committee held a hearing on the issue, as did a federal judge considering a lawsuit brought by a conservative legal group, Judicial Watch.

“If they didn’t take the steps necessary to prevent that happening again, then somebody needs to be held accountable,” the group’s president, Thomas Fitton said yesterday. “Certainly, that’s intriguing.”

The Clinton White House e-mails were reconstructed at a cost of several million dollars.