The Pentagon says the top American commander in Afghanistan, Gen. John Allen, is under investigation for alleged "inappropriate communications" with Jill Kelley, the woman who is said to have received threatening emails from Paula Broadwell, the woman with whom former CIA Director David Petraeus had an extramarital affair.

Defense Secretary Leon Panetta says the FBI referred the matter to the Pentagon on Sunday. Panetta says he ordered a Pentagon investigation of Allen on Monday.

A senior defense official, who discussed the matter only on condition of anonymity because it is under investigation, 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.

Petraeus resigned as CIA director on Friday.