VIDEO - Alleged CIA China turncoat Lee may have compromised U.S. spies in Russia too - NBC News

A man (right, wearing blue tie) identified by local Hong Kong media as former CIA agent Jerry Chun Shing Lee stands in front of a member of security at the unveiling of Leonardo da Vinci's 'Salvator Mundi' painting at the Christie's showroom in Hong Kong on on Oct. 13, 2017. Anthony Wallace / AFP - Getty Images file

"No single officer had access to all of them," one official said.

Investigators soon began to conclude that its communications system for covert communications, referred to as "covcom," had been infiltrated. One theory is that Lee may have helped the Chinese do that. But two former officials said the CIA's system for exchanging messages with its agents was shockingly primitive and subject to easy penetration by the Chinese.

"All they had to do was get one agent's laptop, and they could figure it out," one former official said.

Soon after the task force concluded the Chinese had penetrated covcom, it got an even more troubling report: That after a joint training session between Chinese and Russian intelligence officers, the Russians "came back saying we got good info on covcom," as the former official put it.

Investigators began examining cases of U.S. assets in Russia who had disappeared. Officials concluded they had to change their system for agent communications.

Eventually, Mark Kelton, the CIA's top counterintelligence official, had to brief the leaders of the House and Senate intelligence committees on the damage, some of whom vented their fury behind closed doors. But few others were aware of it, even within the confines of the CIA and FBI. The New York Times reported on the case last year, including the detail that authorities suspected a former CIA officer living in an Asian country.

Last week, for reasons that still are not clear, Lee flew from Hong Kong to New York, where he was met by an FBI team.

The CIA declined to comment, as did Kelton, who was the top counterintelligence official at time.

Ed O'Callaghan, a senior prosecutor in the Justice Department's National Security Division, called Lee's capture "a very important arrest." During an unrelated appearance at the White House earlier this week, he said that although Lee was charged with illegally retaining classified information, "As that case proceeds through the courts, I would expect that more information about the conduct that underlies those charges and the complaint will come out."

Lee appeared briefly in a Brooklyn federal courtroom Monday after his arrest at JFK airport. As early as next week, he will be brought to a courtroom in Alexandria, Virginia, where he will be formally prosecuted, officials said.

Lee's attorney declined to comment.