Former CIA agent Jerry Chun Shing Lee, 53, was arrested Monday night after stepping off a plane at JFK International Airport. He made a brief appearance before a federal judge in New York on Tuesday, but will face charges of unauthorized possession of classified documents in northern Virginia where the CIA is headquartered.

Lee served in the US Army from 1982 to 1986 and worked as a case officer in the CIA from 1994 to 2007. He held various overseas postings and was trained in surveillance detection, recruiting, and handling assets and classified material, among other things.

Read more: US man accused of leaking top-secret documents to China

The FBI obtained warrants to search Lee's luggage and hotel rooms during trips to Virginia and Hawaii in 2012, according to the Justice Department.

"Agents found two small books containing handwritten notes that contained classified information, including but not limited to true names and phone numbers of assets and covert CIA employees, operational notes from asset meetings, operational meeting locations and locations of covert facilities," the Justice Department said.

It's unclear why the FBI did not charge Lee when the search revealed that he was in possession of secret and top-secret information. He was interviewed five times by FBI agents in 2013 but never revealed that he possessed the books.

Lee faces up to 10 years in prison if convicted of possessing secret and top-secret information.

Decimated spy network

An eight-page FBI affidavit makes no allegations of espionage against Lee, although the case is thought to be linked to the decimation of the US intelligence operation in China. The New York Times first reported last year that, between 2010 and the end of 2012, Chinese officials killed "at least a dozen" CIA sources inside China and imprisoned at least six others.

The intelligence meltdown provoked heated debate inside the CIA. Some thought that their network had been wiped out by a mole inside the agency, others speculated that the agents were simply done in by sloppy work, and still others thought the Chinese government had hacked into the CIA computer network.

Read more: Reports: China-linked hackers expose sensitive US military and intelligence data

The CIA launched a hunt for a mole inside the agency, which led to one person, a "former operative" now living elsewhere in Asia, according to the newspaper. But there was not enough evidence to arrest him.

A federal public defender who represented Lee at Tuesday's court hearing declined to comment.

Likewise, CIA spokesman Dean Boyd refused to comment on the case late Tuesday, citing Lee's pending prosecution.

bik/sms (AP, Reuters, AFP, dpa)