Lee had his initial appearance in the Eastern District of New York at 2 p.m. Tuesday. He is not contesting extradition to Virginia, where he will be charged in Alexandria federal court. He does not yet appear to have an attorney.
Lee has been a suspect in a long-running probe to determine if a mole inside the U.S. intelligence community had led to the deaths of a number of CIA assets in China, according to people with knowledge of the probe, which was first reported by the New York Times. He has not been charged with any crimes in connection with those deaths.
People familiar with the matter said that Lee's arrest would be greeted as cause for celebration among current and former CIA officials. But they said it would be hard to prove in court that Lee had provided the information that proved so damaging to the agency's operations.
Lee, a naturalized U.S. citizen and Army veteran, joined the CIA as a case officer in 1994, according to an affidavit from an FBI agent. He had a top secret security clearance and had been given access to sensitive intelligence information. He lost that clearance when he left the agency in 2007.
In 2012, Lee moved to Virginia with his family from Hong Kong, stopping in Honolulu on the way, according to the affidavit. Law enforcement searched his hotel rooms in both places and say they found two small books, a datebook and an address book, filled with handwritten classified information: meetings with CIA assets, meeting locations, operational phone numbers, true names of assets and undercover CIA employees, and the addresses of CIA facilities, including covert ones.
The 49-page datebook and the address book, according to the affidavit, were in a small clear plastic travel pack in Lee's luggage.
Some of the information was secret, and at least one item in the books was top secret, according to the FBI.
Lee was interviewed by FBI agents on five separate occasions in or around May and June 2013, according to the affidavit. He also maintained contact with former CIA colleagues and other government employees. At no point did he reveal the existence of the notebooks.
He left the United States again in June 2013, according to the affidavit. Since then, returning Lee to the United States has been a top priority for the CIA, said the people familiar with the matter. He was living in Hong Kong before his arrest at John F. Kennedy International Airport.
He was not lured back to the United States for arrest but had returned for his own reasons, according to two people familiar with the investigation.
Lee served in the U.S. Army from 1982 to 1986, according to prosecutors. After that he went to Hawaii Pacific University, where he graduated in 1992 with a bachelor's degree in international business management and in 1993 got a master's degree in human resource management.
Matt Zapotosky and Devlin Barrett contributed to this report.