Robin L. Raphel testifies during a Senate Foreign Relations Committee hearing on Capitol Hill in 2004. (Mark Wilson/Getty Images)

A veteran State Department diplomat and longtime Pakistan expert is under federal investigation as part of a counterintelligence probe and has had her security clearances withdrawn, according to U.S. officials.

The FBI searched the Northwest Washington home of Robin L. Raphel last month, and her State Department office was also examined and sealed, officials said. Raphel, a fixture in Washington’s diplomatic and think-tank circles, was placed on administrative leave last month, and her contract with the State Department was allowed to expire this week.

Two U.S. officials described the investigation as a counterintelligence matter, which typically involves allegations of spying on behalf of foreign governments. The exact nature of the investigation involving Raphel remains unclear. She has not been charged.

A spokesman for Raphel said she was cooperating with investigators but has not been told the “scope or nature or that she is the target” of any probe.

U.S. officials spoke on the condition of anonymity because the investigation is ongoing. Spokesmen with the FBI and the Justice Department’s National Security Division declined to comment.

Details of federal counterintelligence investigations are typically closely held and the cases can span years. Although Raphel has spent much of her career on Pakistan issues, it was unknown whether the investigation, being run by the FBI’s Washington Field Office, was related to her work with that country.

“We are aware of this law enforcement matter,” State Department spokeswoman Jen Psaki said. “The State Department has been cooperating with our law enforcement colleagues.”

“She is no longer employed by the State Department,” Psaki said.

Raphel did not respond to attempts to reach her by phone and e-mail. Her daughter also declined to comment, instead referring questions to a family spokesman.

The spokesman, Andrew Rice, said Raphel’s security clearances were put on hold last month and that she is no longer employed by the State Department.

“She is aware and can confirm there is some kind of investigation,” he said.

Rice declined to say whether Raphel had hired a lawyer and refused to answer questions about her whereabouts.

U.S. officials acknowledged that the FBI conducted a search at Raphel’s home Oct. 21 but would not provide details of the search. Agents removed bags and boxes from the home, but it is not clear what was seized there or at her office.

At the State Department, Raphel’s office remained dark and locked Thursday.

At the time of the raid, Raphel was a senior adviser on Pakistan for the office of the special representative on Afghanistan and Pakistan. In that job, she was chiefly responsible for administering nonmilitary aid such as U.S. economic grants and incentives.

The 67-year-old longtime diplomat was among the U.S. government’s most senior advisers on Pakistan and South Asian issues. She is a former assistant secretary of state for South Asia and a former ambassador to Tunisia. At the time of the FBI search of her house, she had retired from the Foreign Service but was working for the State Department on renewable, limited contracts that depended in part on her security clearances.

As a prominent woman among a generation of mostly male diplomats and the former wife of a storied U.S. ambassador, Arnold Raphel, she was among the most recognizable State Department officials and a well-liked and often outspoken career diplomat.

Arnold Raphel was U.S. ambassador to Pakistan when he was killed aboard a plane carrying then-Pakistani President Mohammed Zia ul-Haq in 1988. The cause of the mysterious plane crash has never been proved, but the crash is widely assumed to have been an assassination of the military dictator.

Robin Raphel was divorced from Arnold Raphel when he died. She was then a State Department political officer serving in South Africa but had spent earlier portions of her career in Pakistan. She was also posted in Washington, Britain, India and elsewhere. In 1993, then-President Bill Clinton named her as the first assistant secretary of state for South and Central Asian affairs.

Raphel began her government career as a CIA analyst, according to a State Department biography. She served 30 years in the Foreign Service and retired from the State Department in 2005. She returned to the State Department in 2009 to work as an adviser to Richard Holbrooke, who had been named by then-Secretary of State Hillary Rodham Clinton to the new post of special representative for Afghanistan and Pakistan.

Prior to returning to the State Department, Raphel worked as a lobbyist for Cassidy & Associates, a Washington-based government relations firm. She represented Pakistan, Equatorial Guinea and Iraq’s Kurdistan Regional Government, according to federal disclosure forms.

A spokesman for Cassidy said the firm had not been contacted by the U.S. government about Raphel and was unaware of any investigation related to its former employee.

Espionage cases involving State Department officials are relatively rare. In the last major case, a former State Department official, Walter Kendall Myers, was sentenced in 2010 to life in prison after he and his wife, Gwendolyn Steingraber Myers, were convicted on charges of spying for Cuba over three decades. She received nearly seven years in prison.

The pair provided “highly classified U.S. national defense information” to Cuba, according to the Justice Department.

Missy Ryan and Julie Tate contributed to this report.