Jerry Chun Shing Lee, aka Zhen Cheng Li, 53, was arrested on Monday night after arriving at John F Kennedy International Airport in New York, the Department of Justice said.
A naturalised US citizen, Lee is currently residing in Hong Kong. He worked for the CIA between 1994 and 2007.
Lee, who made his initial appearance in the Eastern District of New York, is charged with unlawful retention of national defence information and faces a maximum penalty of 10 years in prison, if convicted.
According to court documents, in August 2012, Lee and his family left Hong Kong to return to the United States to live in northern Virginia.
While travelling back to the United States, Lee and his family had hotel stays in Hawaii and Virginia.
During his hotel stays, FBI agents conducted courtauthorised searches of Lee's room and luggage, and found that Lee was in unauthorised possession of materials relating to the national defence, the Department of Justice said.
"Specifically, 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 Department of Justice said.
The New York Times said Lee helped China dismantle United States spying operations and identify informants.
Lee's arrest capped an intense FBI inquiry that began around 2012, two years after the CIA began losing its informants in China, the daily said.
According to court papers, Lee's datebook contained handwritten information pertaining to, operational notes from asset meetings, operational meeting locations, operational phone numbers, true names of assets, and covert facilities.
The address book contained true names and phone numbers of assets and covert CIA employees, as well as the addresses of CIA facilities.
"The CIA classification authority determined that the books contained classified information, up to and including secret information and, in at least one instance," the federal complaint said.
The New York Times reported that more than a dozen CIA informants were killed or imprisoned by the Chinese government which was a major set back for its operations in China.
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