The lawsuit, filed in U.S. District Court, accuses the agencies of violating the Privacy Act and selectively leaking "misleading information designed to convince the public that Dr. Lee had engaged in espionage activities for the People's Republic of China."
The suit, which was brought by Lee and his wife Sylvia, does not specify monetary damages. But it opens a second front of legal attack for the jailed scientist, who was charged earlier this month with 59 felonies alleging he removed nuclear secrets from Los Alamos. The indictment didn't allege he gave any information to China.
In a statement, the Lee family said they are "particularly concerned that the unlawful leaks engaged in by the defendants are continuing and will potentially have prejudicial impact on Dr. Lee's ability to defend himself."
The family said they wanted to make the agencies accountable for "deliberate and consistent disclosure of distorted information" about the nuclear scientist. "The government has acknowledged that it has no evidence that Dr. Lee provided any classified information to any unauthorized party," the family added.
In making a case against the government agencies, the suit cites recent Associated Press articles that disclosed that the FBI had doubts as early as November 1998 that Lee was a Chinese spy, but that agents continued to pursue him for many more months amid continued leaks portraying him as a spy.
The indictment eventually brought against Lee accused him of downloading a wide array of nuclear secrets from Los Alamos computers and illegally removing them from the lab on computer tapes. It offered no evidence that Lee gave the information to a foreign government.
China has steadfastly denied stealing secret U.S. nuclear data and Lee denied passing any secrets to China. He was not charged with espionage and has pleaded not guilty to the charges of mishandling secret nuclear data.
Brian Sun, a California attorney representing the Lee family, said Sunday that his clients tried months ago to get the federal agencies to stop news media leaks.
"The Lees were very concerned about this biased and unfair media coverage and requested that this activity stop, but they were unsuccessful," said Sun, who has represented other prominent Asian-Americans, including Democratic fund-raiser Johnny Chung.
An FBI spokesman was not available for comment Sunday, the bureau said. An Energy Department spokeswoman said she hadn't seen the lawsuit, but that the department doesn't believe there is "a valid basis for such a claim."
The suit comes at a sensitive time for federal authorities.
FBI Director Louis Freeh persuaded Congress last week not to hold hearings that could divulge government dissension and oubts in the China espionage investigation, fearing such disclosures might help Lee's defense.
Senate investigators had gathered internal FBI memos, including one addressed to Freeh, that showed agents doubted more than a year ago that Lee had passed nuclear secrets to China. The memos analyzed and identified flaws in the original Energy Department investigation that placed Lee as a suspect.
Senate investigators have been reviewing whether the FBI and Energy Department focused too narrowly on Lee and the Los Alamos lab during the first three years of the investigation, excluding other possible suspects and sites.
The FBI recently refocused its investigation on other labs, facilities and suspects.