In an e-mail memo Friday to the newspaper's staff, Executive Editor Bill Keller said that until Special Counsel Patrick Fitzgerald subpoenaed Miller in the criminal probe, "I didn't know that Judy had been one of the reporters on the receiving end" of leaks aimed at Bush administration critic Joseph Wilson.
"Judy seems to have misled" Times Washington bureau chief Bill Taubman about the extent of her involvement, Keller wrote.
Taubman asked Miller in the fall of 2003 whether she was among the reporters who had gotten leaks about the identity of covert CIA officer Valerie Plame.
"Ms. Miller denied it," the newspaper reported in a weekend story.
Miller and Vice President Dick Cheney's chief of staff, I. Lewis "Scooter" Libby, discussed Wilson and his wife, Valerie Plame, in three conversations in the weeks before the CIA officer's status was outed by columnist Robert Novak.
Keller said he might have been more willing to compromise with Fitzgerald over Miller's testimony "if I had known the details of Judy's entanglement with Libby."
In response, Miller told the Times that Keller's memo was "seriously inaccurate," the newspaper said in a story for Saturday editions. It reported that in a memo to Keller, Miller wrote she "never meant to mislead Phil (Taubman), nor did I mislead him."
As for Keller's remark about "my `entanglement' with Mr. Libby, I had no personal, social, or other relationship with him except as a source," Miller wrote.
Miller's attorney, Bob Bennett, told The Washington Post that it was "absolutely false" to suggest she withheld information about a June 2003 meeting with Libby, saying the conversation hadn't seemed like "a big deal at the time."
Responding to Keller's memo, Bennett said: "I am very concerned now that there are people trying to even old scores and undercut her as a heroic journalist."
Bennett did not return calls by The Associated Press seeking comment.
The criticism of the reporter came amid a sign that the prosecutor may be preparing indictments. Also late this week, Fitzgerald's office set up a Web site containing the record of the broad investigative mandate handed to him by the Justice Department at the outset of his investigation two years ago.
Unlike some of his predecessors who operated under a law that has since expired, Fitzgerald does not need to write a final report, so he would not need a Web site for that purpose.
The criticism of Miller emerged amid new details about how she belatedly turned over notes of a June 23, 2003, conversation she had with Libby.
In her first grand jury appearance Sept. 30 after being freed from prison for refusing to testify, Miller did not mention the meeting.
She retrieved her notes about it only when prosecutors showed her White House visitor logs showing she had met with Libby in the Old Executive Office Building adjacent to the White House, said two lawyers, speaking on condition of anonymity because of the ongoing secrecy of the grand jury probe.
One lawyer familiar with Miller's testimony said the reporter told prosecutors at first that she did not believe the June meeting would have involved Plame because she had just returned from covering the Iraq war. She said she was probably giving Libby an update of her experiences there, the lawyer said.
However, in reviewing her notes, Miller discovered they indicated that Libby had given her information about Plame at that meeting. Fitzgerald then arranged for her to return to the grand jury to testify about it, the lawyers said.
The evidence of that meeting has become important to the investigation because it indicates that Libby was passing information to reporters about Plame well before her husband went public with accusations that the Bush administration had twisted pre-war intelligence on Iraq.
Libby and Bush political adviser Karl Rove have emerged as central figures in the probe because both had contacts with reporter who ultimately disclosed Plame's identity in news stories.
Conflicts between presidential aides' testimony and other evidence could result in criminal charges. The grand jury investigating the matter for the last two years is set to expire next Friday.