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.


U.S. Marine General John Allen (R), the chief U.S. and NATO commander in Afghanistan (Alex Wong/Getty Images)

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.

FBI says agents at the home of Petraeus lover

The FBI isn't saying what it was looking for at Broadwell's home, the biographer whose affair with retired Gen. David Petraeus led to his resignation as CIA director.

FBI agents searched Broadwell's North Carolina home Monday night, and appeared to have been carrying cardboard boxes used for evidence gathering.

(Copyright 2012 by The Associated Press. All Rights Reserved.)