Karl Wagner, a retired CIA officer who had a key role in raising concerns that a White House aide, E. Howard Hunt, was using CIA materials for illegal domestic spying activities during the Watergate era, died Oct. 23 at a retirement community in Carmel, Calif. He was 90. The cause was a cerebral hemorrhage, said a niece, Ann Rodgers Redd.

After joining the CIA in 1950, Mr. Wagner had overseas assignments in Asia and Europe before becoming the executive assistant to the agency’s deputy director, Robert E. Cushman Jr., in 1969.

In that post, Mr. Wagner learned that Hunt, a former CIA operative, had met with Cushman to obtain clandestine materials while conducting a covert operation for the White House under President Richard M. Nixon in August 1971.

The mission was later revealed to be the staged break-in of the office of Lewis Fielding, the psychiatrist of Daniel Ellsberg. Ellsberg was a former Pentagon official who had angered the Nixon administration by leaking the Pentagon Papers, a top-secret history of the Vietnam War, to the media.

In an Aug. 27, 1971, memo to Cushman, Mr. Wagner raised questions about the legality of CIA involvement in domestic clandestine activity.

Mr. Wagner died Oct. 23 at 90. (Courtesy of Central Intelligence Agency)

“Hunt’s use of unique clandestine equipment in domestic activity of an uncertain nature . . . has potential for trouble,” he wrote. He instructed the agency’s technical services division to refuse any of Hunt’s further inquiries and urged Cushman to contact the White House to “obtain assurance that Hunt’s latest caper is ok.”

“Even then,” Mr. Wagner added, “this does not relieve the Agency from its vulnerability if associated with domestic clandestine operations against Americans.”

The same day, Cushman received assurances from White House adviser John D. Ehrlichman that he would handle Hunt and “call a halt to this.”

After the break-in of Fielding’s office on Sept. 3, 1971, Mr. Wagner produced transcripts of Cushman and Ehrlichman’s conversation, along with his original memorandum. The document has been cited as evidence of the CIA distancing itself from the Nixon administration’s Watergate scandal. Mr. Wagner later provided testimony to a congressional committee investigating Watergate.

In 1974, Mr. Wagner received the CIA’s Intelligence Medal of Merit. The citation praised his “personal integrity” and noted that his “exceptional perception and courage of action under very awkward circumstances helped to bring about the cessation of support to an operation which proved to be beyond the jurisdiction of the Agency.”

Karl Wagner was born on March 8, 1924, in Milwaukee, and raised in Evanston, Ill. His father was a partner at the Arthur Andersen accounting firm in Chicago, and his mother was a librarian.

Mr. Wagner served as an Army intelligence officer during World War II. Fluent in German, he did translation work and interrogated German prisoners of war. His military decorations included a Bronze Star Medal.

He retired from the CIA in 1976 as executive assistant to Cushman’s successor, Vernon A. Walters. He moved to Jackson Hole, Wyo., in 1980, and settled in Carmel in 1997.

His wife of 52 years, fellow CIA officer Mary Bottomley Wagner, died in 2007. Survivors include a sister, Janet Morse of Carmel.