The anguish among New York Times staffers over the paper's handling of the Judith Miller saga has mounted in recent days, much to the consternation of its top executives.

"Of course I'm concerned by the very palpable frustration in the newsroom," Executive Editor Bill Keller said yesterday. "I share it. It's excruciating to have a story and not be able to tell it, and annoying to be nibbled at by the blogs and to watch preposterous speculation congeal into conventional wisdom."

As Miller, who served 85 days in jail in the CIA leak case, finished her grand jury testimony yesterday, she returns to a newspaper that has been torn by anger and confusion, not just over her conduct and dealings with Vice President Cheney's chief of staff, but over the way the paper has handled a story in which it has played a central role.

"A lot of the reporters have really been wondering and doubting their editors," said Adam Clymer, a former Times political editor and chief Washington correspondent. "It wasn't that they knew the defense of Judy was wrong, but they didn't have a sense of what was being defended. . . . People all over the paper think the Times should have been covering the story harder."

George Freeman, the Times Co.'s assistant general counsel, met with the Washington bureau last week to address staff complaints. "There was so much rumor and untruth and speculation going around," Freeman said. "I wouldn't characterize it as people being unhappy. People had a lot of questions and concerns. I hope to some degree I assuaged the concerns."

The Times has a team of journalists working on a major piece on the subject, under the supervision of Deputy Managing Editor Jonathan Landman, but has maintained it was impossible to publish such an article until Miller no longer faced legal liability from special prosecutor Patrick Fitzgerald and could cooperate with the paper's reporters. That stance -- challenged by critics who note there is no legal bar to a witness discussing her own grand jury testimony -- has left a vacuum.

"Within the Times, there's a great deal of concern about how this is going to reflect on the Times as an institution and therefore on them," said Alex Jones, a former Times reporter and now a Harvard media analyst. "Everybody wants a clean breast." He said of the editors: "Why they decided they could not speak, I really do not understand."

But Keller said yesterday that the paper was hamstrung by Miller declining, on the advice of her lawyers, to discuss what she told the grand jury. "It's very hard to disentangle the story of Judy's ordeal from the story of her testimony. It's hard to appraise, or even relate, the paper's handling of this case without some sense of what happened during those encounters with her source. I know it's hard because we've tried.

"And despite the understandable yearning for a simple parable, this is a complicated narrative involving a large cast of editors, lawyers and other officials of the paper, and involving imperfect human memories and differing points of view. We'll do our best to tell that story. And I hope we will do it justice."

Miller never wrote an article about the 2003 efforts of White House officials to disclose that Valerie Plame, wife of administration critic Joe Wilson, was a CIA operative. NBC's Tim Russert, Washington Post reporters Glenn Kessler and Walter Pincus, and Time's Matthew Cooper all testified in the case under waivers of confidentiality from their sources.

But Miller refused to accept a waiver from her source, Cheney aide I. Lewis "Scooter" Libby, because she did not consider it voluntary. Miller left an Alexandria jail two weeks ago, agreeing to testify after Libby wrote her a letter and assured her by telephone that he was voluntarily releasing her from her pledge of confidentiality. That, in turn, made many journalists, inside and outside the Times, wonder why she had gone to jail in the first place.

"It isn't clear to me, and it isn't clear to people at the paper, exactly why the waiver wasn't acceptable in its earlier form when other people found ways to find it acceptable," Clymer said.

Interviews with nearly a dozen Times staffers, all of whom refused to be identified because they did not want to openly challenge their bosses, provided a mixed picture. Some said the newsroom is more demoralized now than during the 2003 debacle over Jayson Blair's serial fabrications, because top editors were deceived by Blair but in this case have embraced Miller's handling of the controversy and level of disclosure. The Blair revelations sparked a staff revolt against the autocratic management style of executive editor Howell Raines, who was ousted and replaced by Keller, a former managing editor.

While some staffers say Keller and Publisher Arthur Sulzberger Jr. have allowed their passionate defense of Miller to cloud their journalistic judgment in pursuing the story, others, who respect Keller's more collegial management style, give them the benefit of the doubt for delaying a definitive account.

Miller has long been a lightning rod for her coverage -- some of which turned out to be wrong -- of whether Iraq had weapons of mass destruction before and soon after the U.S. invasion. But Clymer said some of the animosity stems from her tenure as a deputy Washington bureau chief in the late 1980s, when he said Miller tried to force several reporters to leave the bureau.

"Judy is a very aggressive, hard-driving reporter," Clymer said. "She often demands that people do things, and bruises feelings. People in the Washington bureau tried unsuccessfully to persuade editors that her reporting about weapons of mass destruction was wrong."

Some media analysts intensified their criticism when the Times got scooped online, first on the story of Miller's release from jail and again on her discovery of additional, earlier notes of a conversation with Libby, which triggered yesterday's second appearance before the grand jury.

Jay Rosen, a New York University journalism professor, said on his PressThink blog that the Times "has lost the capacity to tell the truth about itself in this story. . . . What we don't know is why the Times has gone into editorial default."

American Journalism Review Editor Rem Rieder wrote on his magazine's Web site that the longer the Times waits, "it begins to look like there's something to hide. And credibility accrues to those nasty theories that Miller really went to jail to salvage her reputation in the wake of the botched WMD coverage."

Times columnist Frank Rich said in a CNN interview that he has been "frustrated" by the situation: "I think the Times, now that she has testified, has to be transparent about what happened, why her situation was different from Matt Cooper's, and indeed ultimately about her grand jury testimony, which, as I understand it legally, she's free to disclose, or will be presumably after Mr. Fitzgerald is finished with her."

After her release from jail Judith Miller was greeted at the New York Times by Publisher Arthur Sulzberger Jr., left, Executive Editor Bill Keller and, doing the hugging, Managing Editor John Geddes.