The career of Gen. John Allen, the top U.S. commander in Afghanistan, is now in jeopardy due to the investigation of the David Petraeus sex scandal.

The Pentagon said Tuesday that Allen is under investigation for alleged “inappropriate communications” with Jill Kelley, the woman who is said to have received threatening emails from Petraeus’ paramour.

Defense Secretary Leon Panetta said in a written statement issued to reporters aboard his aircraft, en route from Honolulu to Perth, Australia, that the FBI referred the matter to the Pentagon on Sunday.

Panetta said he ordered a Pentagon investigation of Allen on Monday.

A senior defense official traveling with Panetta said Allen’s communications were with Kelley, who has been described as an unpaid social liaison at MacDill Air Force Base, Fla., which is headquarters to the U.S. Central Command. She is not a U.S. government employee.

Kelley is said to have received threatening emails from Paula Broadwell, who is Petraeus’ biographer and who had an extramarital affair with Petraeus that reportedly began after he became CIA director in September 2011.