The officials, who spoke on the condition of anonymity because they were not authorized to discuss an ongoing investigation, did not give details about why they were examining Ms. Raphel’s activities. Nor did they say whether she was officially a target of the investigation.

It is extremely rare for the F.B.I. to open a counterintelligence investigation into such a prominent Washington figure. Any decision by the Justice Department to open the inquiry would have had to take into account that an investigation — whatever its outcome — will have a lasting impact on Ms. Raphel’s ability in the future to operate within American diplomatic circles. One official said on Friday that Ms. Raphel had been stripped of her security clearances as part of the investigation.

Jen Psaki, the State Department spokeswoman, said in a statement that the department was “cooperating with our law enforcement colleagues on this matter.”

“Ms. Raphel’s appointment expired,” Ms. Psaki said. “She is no longer a department employee.”

Andrew Rice, a spokesman for Ms. Raphel, said that she had not been informed whether she was a target of the investigation, adding that “her nearly 40 years of public service at the highest levels of U.S. diplomacy speak for themselves.”

“I’m confident this will be resolved,” Mr. Rice said.

The Washington Post first reported the investigation on its website Thursday night.