Mr Lee was named by the New York Times earlier this year as the chief suspect in the alleged theft of nuclear secrets from the US National Laboratory at Los Alamos over the past 20 years. The stolen secrets were believed to include the computer blueprint for a miniaturised nuclear warhead, the W-88, which the Chinese appeared to have replicated.
Mr Lee was first suspended, and then dismissed, from his post in the top-secret nuclear weapons design department, but was not charged until yesterday. Before he lost his job, he had taken, and failed, two lie detector tests and been described by FBI agents who questioned him as uncooperative and obstructive. He and his wife had also taken trips to China.
The allegations came to light in the course of a US Congressional investigation into claims that China had succeeded in penetrating US nuclear security. While the report, compiled by Representative Christopher Cox, focused on security at the Los Alamos laboratory and singled out Wen Ho Lee as the likely culprit, Mr Lee himself has consistently protested his innocence.
He has admitted transferring top-secret files from his high-security computer to a less secure computer in his office, but says that this was a common practice. He has categorically denied passing information to China, and says that the trips he made to China were all cleared by the authorities at the laboratory.His lawyer has argued on his behalf that, as the only Asian in his department, he was unfairly targeted by the investigation.
A series of subsequent investigations, including one commissioned by the White House, cast doubt on the allegations and found that Wen Ho Lee's department was not the only repository of the information allegedly stolen by China.
The precise nature of the charges against Mr Lee was not divulged yesterday. But if, as it appears, they are restricted to the mishandling of classified information - however valuable - prosecutors could find it hard to obtain a conviction.
A former head of the CIA, John Deutch, lost his security clearance this summer after he admitted removing classified and highly sensitive files from his office computer and taking them home. He was subject to a severe reprimand, but was not prosecuted.
The case of Wen Ho Lee has opened wide political divisions in the United States. Some believe that he is the most dangerous spy since the Cold War. Others, including Americans of Asian origin, fear that he is the victim of a politically and racially inspired witch-hunt.