The FBI investigation that led to the resignation of CIA Director David Petraeus has expanded to include Gen. John Allen, commander of U.S. and NATO troops in Afghanistan, the Pentagon said early today.

<WC1>Allen is under investigation for alleged "inappropriate communications" with <WC>Jill Kelley of Tampa, Fla., who prompted the FBI inquiry after complaining of threatening emails that turned out to be from <WC1>Paula Broadwell, with whom Petraeus had an extramarital affair.

<WC>According to a senior Pentagon official, the FBI uncovered <WC1>20,000 to 30,000 pages of emails and other documents from Allen's communications with Kelley between 2010 and 2012. He would not say whether they involved sexual matters or whether they are thought to include unauthorized disclosures of classified information. He said he did not know whether Petraeus is mentioned in the emails.

Allen, a four-star Marine general, succeeded Petraeus as the top <WC>U.S.<WC1> commander in Afghanistan in July 2011.

"Gen. Allen disputes that he has engaged in any wrongdoing in this matter," the official said.<WC>

<WC1>He said Allen currently is in Washington.

Defense Secretary Leon Panetta said in a statement issued to reporters aboard his <WC>jet <WC1>en route from Honolulu to Perth, Australia, that the FBI <WC>on Sunday <WC1>referred the <WC>Allen <WC1>matter to the Pentagon <WC>and on Monday he <WC1>ordered a Pentagon investigation of Allen.

Panetta said that while the matter is being investigated by the Defense Department<WC>'s<WC1> <WC>i<WC1>nspector <WC>g<WC1>eneral, Allen will remain commander of the International Security Assistance Force, based in Kabul. He praised Allen as having been instrumental in making progress in the war.

The FBI's decision to refer the Allen matter to the Pentagon rather than keep it itself, combined with Panetta's decision to allow Allen to continue as Afghanistan commander without a suspension, suggested that officials viewed whatever happened as a possible infraction of military rules rather than a violation of federal criminal law.

<WC>But <WC1>Panetta said Allen's nomination to be the next commander of U.S. European Command and the commander of NATO forces in Europe has been put on hold "until the relevant facts are determined." He had been expected to take that new post in early 2013, if confirmed by the Senate, as had been widely expected.

Panetta said President Barack Obama was consulted and agreed Allen's nomination should be put on hold.<WC>

<WC1>Allen was to testify at his confirmation hearing <WC>Thursday <WC1>before the Senate Armed Services Committee. Panetta said he asked committee leaders to delay that hearing.

Panetta also said he wants the <WC>c<WC1>ommittee to act promptly on Obama's nomination of Gen. Joseph Dunford to succeed Allen as commander in Afghanistan. Dunford's hearing is also scheduled for Thursday.