Story highlights Pakistan expert Ambassador Robin Raphel was working for State Department

Office and home have been searched, officials say

Her security clearance was pulled and her contract has not been renewed, officials say

FBI agents searched the home of veteran diplomat and Pakistan expert Ambassador Robin Raphel in October as part of a counterintelligence investigation, three U.S. government officials told CNN.

As part of the investigation, Raphel's State Department office was searched and sealed, two of the officials said. It's unclear whether she is the target of the investigation, or what agents were searching for. The officials said it is an ongoing investigation and no charges have been filed.

"We are aware of this law enforcement matter. The State Department has been cooperating with our law enforcement colleagues," State Department spokesperson Jen Psaki said. Psaki added that Raphel is "no longer a department employee."

At the time of the raid, Raphel, a retired career Foreign Service officer, was an adviser on Pakistan under a limited, renewable contract to the State Department's Special Representative for Afghanistan and Pakistan, where she administered nonmilitary aid and economic grants. It is unclear, however, whether the inquiry is related to her work on Pakistan.

Senior State Department officials said Raphel's security clearance was pulled last month, at which time she was placed on administrative leave. Her contract, which expired on November 2, was not renewed.

The officials describe the investigation as a counterintelligence investigation, which typically refers to allegations of spying on behalf of foreign governments. Officials declined to describe the exact nature of the investigation.

Raphel, the former assistant secretary of state for South Asia and ambassador to Tunisia, spent much of her career working on Pakistan and South Asia. Raphel was well-liked and respected by her colleagues and often outspoken about what she saw as flaws with U.S. policy toward Pakistan.

Raphel's State Department biography says she began her career as a CIA analyst before serving 30 years in the Foreign Service. She retired from the State Department in 2005, but returned in 2009 to work as an adviser to the late Richard Holbrooke, appointed by then-Secretary of State Hillary Clinton as the first special representative for Afghanistan and Pakistan. CNN attempted to contact Raphel, but messages have not been returned.