The New York Times devoted an extraordinary third of a page last week to a review of its coverage of the investigation and prosecution of Wen Ho Lee, the Taiwan-born American nuclear scientist who was held shackled and in solitary confinement without bail for nine months as a dangerous potential spy but finally set free after a plea-bargain agreement.

A memo headed, “From the Editors,” defended The Times’ coverage, against sharp criticism from competing journalists, media critics, defenders of the accused scientist, “who contended that our reporting had stimulated a political frenzy amounting to a witch hunt.” The newspaper expressed pride “on the whole” in its work. It said a review of the coverage “found careful reporting that included extensive cross-checking and vetting of multiple sources, despite enormous obstacles of official secrecy and government efforts to identify The Times’ sources.”

To its credit, The Times also found shortcomings: It should have given Lee the full benefit of the doubt. It could have pushed harder to uncover weaknesses in the FBI case against Lee. It should have moved faster to assess the scientific, technical and investigative assumption that led the FBI and the Department of Energy to connect Lee to an acknowledged major security breech.

The initial story, on March 6, 1999, noted that the government prosecutors did not think they had enough evidence to justify a wiretap on Lee’s telephone. The memo said that fact was “deep in the text” and, instead, “should have been more prominent in the article and in our thinking.”

The memo also mentioned “a problem of tone” in some articles: “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 with knowledge of the case.”

A prime example was an article that said Lee “may be responsible for the most damaging espionage of the post-Cold War era.” The memo said that the statement was accurately attributed to officials and lawmakers, primarily Republicans, but “should have been balanced with the more skeptical views of those who had doubts about the charges against the scientist.”

The memo listed other stories that the editors wished they had assigned early in the investigation: A closer look at the Chinese weapons debate, in which “Republicans were eager to score points against the White House on China.” An examination of how Lee’s handling of classified information compared with the usual practices in the laboratories. A closer look at Notra Trulock, “the intelligence official at the Department of Energy who sounded some of the loudest alarms about Chinese espionage.” An exploration of various suspects and leads that investigators passed up in favor of Dr. Lee.

The Times said blame for the lapses lay, not with reporters, but “principally with those who directed the coverage, for not raising questions that occurred to us only later.” Every reporter needs an editor, especially investigative reporters, who too often take on the views of official investigators and prosecutors.

One excuse offered by The Times was that its stories were “echoed and often oversimplified by politicians and other news organizations.” This shifting of blame neglects a current fact of life in the reporting of national and international affairs: Many other newspapers throughout the country have almost entirely abandoned their own national coverage and rely heavily on The Times and a few other sources for news and interpretation.

When The Times makes a misstep, the effect is felt all over. This example of soul searching can help newspapers do better, to the benefit of everyone.