PERTH, Australia -- In a new twist to the Gen. David Petraeus sexscandal, the Pentagon said Tuesday that the top American commander inAfghanistan, Gen. John Allen, is under investigation for alleged"inappropriate communications" with a woman who is said to have receivedthreatening emails from Paula Broadwell, the woman with whom Petraeushad an extramarital affair.

Defense Secretary Leon Panetta said ina written statement issued to reporters aboard his aircraft, en routefrom Honolulu to Perth, Australia, that the FBI referred the matter tothe Pentagon on Sunday.

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

Asenior defense official traveling with Panetta said Allen'scommunications were with Jill Kelley, who has been described as anunpaid social liaison at MacDill Air Force Base, Fla., which isheadquarters to the U.S. Central Command. She is not a U.S. governmentemployee.

Kelley is said to have received threatening emails fromBroadwell, who is Petraeus' biographer and who had an extramaritalaffair with Petraeus that reportedly began after he became CIA directorin September 2011.

Petraeus resigned as CIA director on Friday.

Allen, a four-star Marine general, succeeded Petraeus as the top American commander in Afghanistan in July 2011.

Thesenior official, who discussed the matter only on condition ofanonymity because it is under investigation, said Panetta believed itwas prudent to launch a Pentagon investigation, although the officialwould not explain the nature of Allen's problematic communications.

Theofficial said 20,000 to 30,000 pages of emails and other documents fromAllen's communications with Kelley between 2010 and 2012 are underreview. He would not say whether they involved sexual matters or whetherthey are thought to include unauthorized disclosures of classifiedinformation. He said he did not know whether Petraeus is mentioned inthe emails.

"Gen. Allen disputes that he has engaged in any wrongdoing in thismatter," the official said. He said Allen currently is in Washington.

Panettasaid that while the matter is being investigated by the DefenseDepartment Inspector General, Allen will remain in his post as commanderof the International Security Assistance Force, based in Kabul. Hepraised Allen as having been instrumental in making progress in the war.

Butthe Allen investigation adds a new complication to an Afghan war effortthat is at a particularly difficult juncture. Allen had just providedPanetta with options for how many U.S. troops to keep in Afghanistanafter the U.S.-led coalition's combat mission ends in 2014. And he wasdue to give Panetta a recommendation soon on the pace of U.S. troopwithdrawals in 2013.

The war has been largely stalemated, withlittle prospect of serious peace negotiations with the Taliban andquestions about the Afghan government's ability to handle its ownsecurity after 2014.

At a photo session with Australian PrimeMinister Julia Gillard shortly after he arrived in Perth, Panetta wasasked by a reporter whether Allen could remain an effective commander inKabul while under investigation. Panetta did not respond.

TheFBI's decision to refer the Allen matter to the Pentagon rather thankeep it itself, combined with Panetta's decision to allow Allen tocontinue as Afghanistan commander without a suspension, suggestedstrongly that officials viewed whatever happened as a possibleinfraction of military rules rather than a violation of federal criminallaw.

Allen was Deputy Commander of Central Command, based inTampa, prior to taking over in Afghanistan. He also is a veteran of theIraq war.

In the meantime, Panetta said, Allen's nomination to bethe next commander of U.S. European Command and the commander of NATOforces in Europe has been put on hold "until the relevant facts aredetermined." He had been expected to take that new post in early 2013,if confirmed by the Senate, as had been widely expected.

Allen wasto testify at his confirmation hearing before the Senate Armed ServicesCommittee on Thursday. Panetta said he asked committee leaders to delaythat hearing.

The senior defense official said Panetta has nottalked to Allen about the investigation, nor has he discussed the matterwith President Barack Obama, although he consulted with unspecifiedWhite House officials before making the decision to seek a postponementof Allen's confirmation hearing.

Panetta did talk about the Allenmatter with Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff,who happens to also be in Perth for a meeting of American and Australiandiplomatic and defense officials. Those talks were starting Tuesdaywith an official dinner.

With a cloud over Allen's head, it wasunclear Tuesday whether he would return to Kabul, even though Panettasaid Allen would remain in command. The second-ranking American generalin Afghanistan is Army Lt. Gen. James Terry.

NATO officials had no comment about the delay in Allen's appointment.

"We have seen Secretary Panetta's statement," NATO spokeswoman Carmen Romero said in Brussels. "It is a U.S. investigation."

Panettaalso said he wants the Senate Armed Services Committee to act promptlyon Obama's nomination of Gen. Joseph Dunford to succeed Allen ascommander in Afghanistan. That nomination was made several weeks ago.Dunford's hearing is also scheduled for Thursday.