Notra Trulock, the Energy Department's deputy director of intelligence attacked a report issued by the agency's inspector general last week that failed to back him up and hold Clinton administration officials responsible for security failures, The Washington Post and The New York Times reported in Tuesday's editions.
"I think the time has come for me to move on," Trulock told the Post.
Trulock could not be reached by telephone for comment Monday night, but the Energy Department confirmed his resignation.
An Energy Department spokesperson issued a statement saying Secretary Bill Richardson was "disappointed" by Trulock's decision. The statment said Richardson believed Trulock "performed valuable work and recently awarded him a $10,000 bonus for his role in helping uncover evidence of espionage and for his persistence in pursuing it."
On the other hand, Richardson stands by the findings of the inspector general's report, she added.
Trulock has come under criticism in recent weeks. Two government reports and other intelligence and security officials questioned whether he should have made a Chinese-American scientist at Los Alamos, Wen Ho Lee, the prime espionage suspect.
Other officials participating in the investigation have said they believe Trulock and the FBI singled out Lee mainly because of his ethnicity. Lee, a Taiwanese-born nuclear physicist and U.S. citizen, has denied the allegations of espionage and has not been charged with any crime.
At least three other Energy Department employees have filed grievances against Trulock for alleged discrimination.
Trulock was demoted to deputy director last year after serving as the Energy Department's intelligence director for four years.
In the Post interview, Trulock denied focusing on Lee because he was Chinese.