US authorities said Tuesday they had arrested a former CIA agent, Hong Kong resident Jerry Chun Shing Lee, after discovering he had an unauthorised notebook that had the identities of undercover US spies.

Lee, a naturalised US citizen also known as Zhen Cheng Li, was arrested late Monday after he arrived at JFK International Airport in New York.

The Department of Justice said Lee, 53, grew up in the United States and served in the US Army before joining the Central Intelligence Agency as a case officer in 1994.

He served in unnamed overseas locations and left the agency in 2007, later apparently taking a job in Hong Kong.

In a complaint filed in a New York federal court, the Justice Department said that in 2012, FBI agents with court-ordered warrants secretly searched Lee's luggage while he was travelling in the United States and found he was carrying top secret materials he was not authorized to have.

"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.

The case takes place amid concern in the US intelligence community that the Chinese government has been able to cripple their operations in that country.

Lee was charged with unlawful retention of national defense information, a charge that can bring up to 10 years in prison.

Officials did not say why it took so long to bring charges against Lee, or whether he had leaked any materials to foreign countries.