Federal investigators told 60 Minutes Correspondent Lesley Stahl that the publicity generated by that article permanently harmed their probe.
And they claim that Trulock misled them by concluding that the Los Alamos National Laboratory, where Lee worked, was the only possible source of the secrets that were apparently funneled to China.
Trulock denies that he misled the FBI. He also rejects accusations that he singled Lee out because of Lee's Chinese ancestry as "preposterous."
Jailed for more than nine months on 58 counts of mishandling secret information, Lee was released in September after he pleaded guilty to one count and agreed to cooperate with investigators.
Trulock was the Energy Department's chief of intelligence in 1995 when he discovered information about the W-88, the most advanced nuclear warhead in the United States' arsenal, in an internal Chinese government report.
After being advised by a panel of scientific experts that the data must have been stolen by or provided to the Chinese illegally, Trulock told the FBI that China had information on the W-88 that may have been obtained through espionage.
But according to secret reviews of the case conducted separately by the FBI and the Justice Department, Trulock also identified the Los Alamos lab as the only possible source of the leak to China.
In the interview, Trulock denied that.
"It's not the way it happened," he said. "I mean, there was no, there was no basis for me to say that at that time, or at any other time down the road."
The Justice Department review also reports that Trulock did not tell the FBI that some experts, including some of Trulock's own advisors, felt the leak may have come from elsewhere.
Investigators told 60 Minutes that Trulock's assertions steered them away from other potential sources of leaks to China: specifically from the Defense Department and the hundreds of contractors who assembled the W-88.
However, Ed Curran, a senior investigator, admitted that the FBI can be faulted for failing to check out Trulock's claims.
"I think we should have gone back at the time and verified that information and conducted interviews," Curran said.
Trulock then gave the FBI a report listing 12 suspects, which contained, according to the Justice Department, "a singular indictment of Wen Ho Lee."
One of the people he reached was Congressman Norm Dicks, in 1998 the ranking Democrat on a special congressional committee investigating Chinese espionage.
"When this was laid out members were stunned by the implications of it," said Dicks. "It just looked like the smoking gun. Everything pointed toward the labs."
Dicks acknowledges that by devoting attention only to Los Alamos, Trulock may have sent federal agents barking up the wrong tree. But he does not believe Trulock intentionally misled the FBI.
"I think he was a true believer," said Dicks. "His mistake was he should have told us that other people disagreed with him."
Trulock didn't stop with Congress. Convinced the Clinton administration worried about relations with China and trying to deal with a campaign finance scandal involving Chinese donations was trying to silence him, he went to the New York Times.
And in March, 1999, the Times ran on its front page a blockbuster story about China stealing nuclear secrets from the laboratory at Los Alamos.
Two days after the story ran, Energy Secretary Bill Richardson fired Lee.
Investigator Curran said the Times story "was just absolutely devastating" to his probe because it put the investigation in the public realm.
And he said the person who leaked the story may have broken laws by releasing classified information to an unauthorized person.
Indeed, Trulock who was reassigned in 1998 and eventually quit is under investigation for disclosing classified information in a manuscript he wrote called The Nuclear Spy Follies.
Trulock claims to have been persecuted by the FBI and that he's the victim a vendetta against him for blowing the whistle on Chinese espionage.
Judicial Watch, a conservative legal foundation that's made its name bringing lawsuits against the Clinton administration, is suing both the FBI and Lee on Trulock's behalf.