In an extraordinary editor's note, the New York Times acknowledged yesterday that its reporting on allegations against scientist Wen Ho Lee contained "flaws" and "a problem of tone" that "fell short of our standards."

By turns self-congratulatory and self-critical, the 23-paragraph statement said the newspaper got most of the facts right when it began reporting espionage allegations against Lee in March 1999. In the frenzy that followed, the Chinese American nuclear scientist was fired from Los Alamos National Laboratory, jailed for nine months and freed two weeks ago after pleading guilty to a single felony--prompting an apology from the federal judge in the case and pointed criticism of the Times by a White House official.

The newspaper blamed others in part, saying that its stories were "echoed and often oversimplified by politicians and other news organizations" and that the Times was not to blame for "stimulating a witch hunt."

But the editors didn't let themselves off the hook. In fact, they made a point of saying that "the blame lies principally with those who directed the coverage," not with the "persistent and fair-minded" reporters--Jeff Gerth, the Pulitzer Prize winner who also broke the Whitewater story, and James Risen--who wrote the original pieces.

The issue of apportioning blame was so sensitive, sources say, that Gerth, Risen and Deputy Washington Bureau Chief Jill Abramson flew to New York last week to hash things out with Managing Editor Bill Keller, whose original note had been scheduled to run Sunday. During a long session, the wording was changed in a way that clearly exonerated the reporters.

Journalists who have followed the story gave the Times decidedly mixed reviews. "It's not often you get an admission of error on that scale," said Lars-Erik Nelson, a New York Daily News columnist who has repeatedly criticized the coverage. But, he said, "they sort of blame this on competing journalists and media critics as though we have some kind of agenda to hurt the Times, as opposed to criticizing poor coverage. The whole thing is defensive."

Timothy Noah, who has assailed the coverage on Slate.com, called the "nonapology apology" an "evolutionary step forward for an institution like the New York Times to acknowledge errors in its reporting that are less simple factual errors or misquotations than they are large errors, having to do with interpretation and especially with believing a source. . . . They characterize as biases in their reporting things that really were examples of them being duped."

"Personally," said ABC's John Donvan, a "Nightline" correspondent who has covered the story, "I kept waiting for them to say they regret the damage to Lee himself." Still, he said of the Times editors, "they looked real hard at themselves. I'm not expecting them to be beating their breast and on their knees. They got a whole lot right and some things factually wrong."

Keller and other executives, who had refused to comment while preparing the modified, limited mea culpa, declined interview requests yesterday as well.

The first Risen-Gerth story--"Breach at Los Alamos: China Stole Nuclear Secrets for Bombs, U.S. Aides Say"--said the government's response "was plagued by delays, inaction and skepticism." The Times said Lee (who was not named until a couple of days later) had failed a lie detector test, which turned out not to be true. The paper also quoted a CIA official as saying the case was "going to be just as bad as the Rosenbergs."

The editorial page soon began castigating Clinton administration officials, calling them "amazingly careless"; demanding to know why an FBI wiretap on Lee was "inexplicably turned down"; questioning the "fitness" of national security adviser Sandy Berger to remain in office, and saying of Attorney General Janet Reno that her accumulated "blunders" would "have led to Ms. Reno's removal in any recent administration other than this one."

As the case against Lee slowly unraveled, the Times brought in new reporters who, without acknowledging any past contradiction, took a more skeptical view of the case. The FBI, meanwhile, concluded that the security breach could have occurred at many facilities, not just Los Alamos. This was a rejection of the inquiry hotly pursued by Energy Department investigator Notra Trulock--who was cited in the original Times report--against Lee and Los Alamos. (Trulock later quit and is now under investigation for allegedly compromising classified information.)

During this media storm, Lee was held shackled in his cell for nine months until the plea agreement under which 58 of the 59 felony counts were dropped. As the case collapsed, a Times editorial demanded an investigation of whether "racial profiling or other unfair tactics were used by the government."

The White House was not pleased. "From the beginning we have cautioned the New York Times and other news organizations that this story was enormously complex, and they should be very careful about overrelying on one side," incoming White House press secretary Jake Siewert said last week. He said Times editors "haven't acknowledged" that "they were part of the machinery in Washington and around the country that created that focus on a particular individual. . . .

"So there's a strange quality to the reporting and the editorials now, which seem to be criticizing the administration for something the paper itself had urged them to do in the early going."

One Lee associate said the editor's note, while welcome, did not go far enough in acknowledging the harm to the 60-year-old scientist.

In the statement on Page A2, the space reserved for corrections, Times executives said they were "proud of work that brought into the open a major national security problem. . . . But looking back, we also found some things we wish we had done differently in the course of the coverage to give Dr. Lee the full benefit of the doubt."

Essentially acknowledging that they were swept away by the hype, the editors said: "In place of a tone of journalistic detachment from our sources, we occasionally used language that adopted the sense of alarm that was contained in official reports and was being voiced to us by investigators, members of Congress and administration officials."

Among other things, the editors said, they should have interviewed more outside scientists and looked more closely at both Trulock and a political atmosphere in which Republicans were trying to score points against the White House. And there should have been "a full-scale profile of Dr. Lee, which might have humanized him and provided some balance."

Asked about yesterday's lengthy statement, Gerth said: "I don't talk about the Times's business, but as a reporter I'm glad that other people talk about theirs."