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A week after the 2008 New York Times article appeared, Mr. Kiriakou told Mr. Martinez in an email that he had complained to the newspaper’s ombudsman that the use of his name was “despicable and unnecessary” and could put his former colleague in danger. He denied to Mr. Martinez that he had cooperated with the Times reporter.

Naming names

A few days before his arrest, in a recorded interview with the FBI, Mr. Kiriakou was told that the defense filing contained the covert officer’s name — the one he provided to “Journalist A.”

“How the heck did they get him?” he asked the FBI. “[The officer] was always undercover. His entire career was undercover.”

The CIA declined to comment to on what effect the disclosure has had on the still-active covert officer’s career or on Mr. Martinez.

Mr. Kiriakou’s naming names unraveled for him when defense attorneys included classified information and the covert agent’s name in a court filing. It prompted the CIA to request Justice to begin an unauthorized-disclosure investigation that resulted in his arrest this month.

Mr. Kiriakou, who worked as a staffer for Sen. John F. Kerry, Massachusetts Democrat, faces four charges, three of which fall under the 1917 Espionage Act for providing classified information to those not authorized to receive it, and one charge under the 1982 Covert Agent Identity Protection Act.

The 2008 New York Times article that named Mr. Martinez and quoted Mr. Kiriakou did not prompt a government investigation. The Justice Department says Mr. Kiriakou was not under investigation until defense attorneys filed the classified legal brief in January 2009.

“This is not a whistleblower case,” Justice spokesman Dean Boyd told The Washington Times. “We simply followed the facts, which led us to the person we believe provided names.”

Since the Sept. 11 attacks, the Justice Department has investigated and brought charges in five cases against former or current government employees who allegedly spilled secrets to reporters. The Obama Justice Department filed charges in all five cases, beginning in December 2009.

Sharon Scranage, a former clerk for the CIA station in Ghana, is the only person convicted under the 1982 protection act. She pleaded guilty to providing names to her boyfriend, a Ghanian intelligence officer, and was given a five-year prison term that later was reduced to two years.

The Kiriakou case stands out because it is the only one of the five that involves providing the name of a covert officer to a journalist.

The case marks the second of the five in which a person has been charged with leaking secrets to a New York Times reporter based on evidence in seized emails between the reporters and sources.

A year ago, former CIA officer Jeffrey Sterling was indicted under the Espionage Act for providing information to reporter and author James Risen about a 1990s classified operation to disrupt Iran’s nuclear program.

In both cases, the Times reporters did not provide any information on their sources to the government.