Clare Edward Petty, a Cold Warrior who built an early reputation in the CIA as a perceptive counterespionage officer but whose career ended when he accused the agency’s highest-ranking spycatcher of being a Soviet mole, died March 18 at an assisted living facility in Atlanta. He was 90 and had dementia.

A decorated World War II combat vet­eran, Mr. Petty joined the fledgling CIA in 1947. Within a few years, he played a key role in identifying and catching Heinz Felfe, one of the most successful Soviet agents of the Cold War.

Felfe was a high-ranking West German intelligence official who raised Mr. Petty’s suspicions with his consistent ability to provide high-quality information about the East German government and Soviet intelligence service. In a business filled with guesswork and hunch, Mr. Petty noticed, Felfe was a little too perfect.

Felfe turned over 15,000 photographs and reams of other intelligence to the Soviets before he was arrested in 1961 and sentenced to 14 years in prison. (He was freed in 1969 in exchange for the release of three West German students who had been jailed for spying in the Soviet Union.)

Mr. Petty’s initial work on Felfe caught the attention of James J. Angleton, the CIA’s counterintelligence chief. In the mid-1960s, he chose Mr. Petty to join an elite group whose mission was to root out a Soviet mole suspected of infiltrating the agency at a high level.

The molehunt was spearheaded and directed by Angleton, who was fiercely suspicious of colleagues. Angleton acted on leads provided by Anatoly M. Golitsyn, a KGB defector; together, the pair’s allegations helped destroy the careers of a number of CIA officers who were fired for alleged misdeeds and later found to be innocent.

“It became an institutional paranoia that permeated the organization for an unfortunate period of time,” said journalist David Wise, author of “Molehunt: The Secret Search for Traitors That Shattered the CIA,” a 1992 book about the agency’s witch-hunt era.

Angleton soon became the target of his own inquisition. As time passed and no high-level mole was snared, Mr. Petty became convinced that Golitsyn was a Soviet-controlled agent providing disruptive misinformation to the CIA. The mole, Mr. Petty reasoned, had to be Golitsyn’s handler: Angleton himself.

Among Mr. Petty’s concerns was Angleton’s once-close relationship with Kim Philby, who rose to the highest levels of the British intelligence service before he was unmasked as a Soviet mole in the early 1960s.

According to his unpublished memoir, Mr. Petty spent more than two years working secretly to investigate his supervisor. He gathered intricate details about Angleton’s movements and close associates through the years, looking for — and finding, he thought — evidence that Angleton could have collaborated with the Soviets.

Mr. Petty admitted that it was a messy conclusion based largely on the circumstantial suggestion of guilt. “It was not a clear-cut case,” he told David Martin for “Wilderness of Mirrors,” Martin’s 1980 book about the Cold War-era CIA.

Whatever his misgivings, Mr. Petty reported concerns about Angleton to agency superiors in 1974. He delivered several drawers full of notes and documents supporting his view, then spent at least 26 hours over the course of a week explaining his work to a senior officer in tape-recorded interviews.

The price of that move was Mr. Petty’s job — he retired almost immediately — and his reputation. His accusation against Angleton was dismissed in a CIA study, and Mr. Petty remains one of the more controversial figures in the agency’s history.

“To this day, there are people who don’t want to hear Ed Petty’s name,” said Mary Ellen Reese, who wrote a 1990 book about the CIA’s work in postwar West Germany. He may not have been right about Angleton, but “he acted out of his conviction regardless of the consequences to him, which he knew would be grave,” she said. “He was a man of real principle and a real patriot.”

CIA Director William E. Colby fired Angleton in December 1974 after New York Times investigative reporter Seymour Hersh revealed that the CIA was illegally conducting counterintelligence activities against antiwar protesters and other domestic groups.

Clare Edward Petty was born Dec. 2, 1920, in Norman, Okla. He was a Phi Beta Kappa graduate of the University of Oklahoma, where he received a master’s degree in political science in 1943.

He served in an Army artillery battalion during World War II. He landed at Normandy shortly after the D-Day invasion and fought his way across France and into Germany. He received five awards of the Bronze Star Medal.

Living in Annapolis in retirement, he sailed the Chesapeake Bay on a boat named Anomaly. He sang for many years in the Annapolis Chorale and the choir of the Naval Academy Protestant Chapel, where he also taught a Bible studies course for adults.

His wife of 67 years, Melba Thompson Petty, died in January. A grandson, Army Capt. Christopher P. Petty, was killed in action in Iraq in 2006.

Survivors include their five children, Paul Petty of Prescott, Ariz., Lora Jeanne Fredrick of Atlanta, Ralph Petty of Pacifica, Calif., Carl Petty of Bethesda and Jim Petty of Lausanne, Switzerland; a sister; a brother; 10 grandchildren; and nine great-grandchildren.