AFP - Getty Images, Reuters
General John Allen, left, pictured in October, and Jill Kelley, seen walking out of her home in Tampa on Monday.
By NBC News staff
U.S. General John Allen, commander of the International Security Assistance Force in Afghanistan, is under investigation over allegations of ?inappropriate? emails between him and the woman who sparked the probe into CIA Director David Petraeus, officials said early Tuesday.
In a statement, the Secretary of Defense Leon Panetta said that the FBI had referred ?a matter involving" Allen to the Department of Defense.
?Today, the secretary directed that the matter be referred to the Inspector General of the Department of Defense for investigation, and it is now in the hands of the Inspector General,? Panetta said.
The statement said that Allen would remain commander of ISAF during the investigation and that he was ?entitled to due process in this matter.?
Emails on 'coming and goings' of Petraeus, other military officials escalated FBI concerns
The FBI eventually discovered that the emails received by Jill Kelley, a close friend of the Petraeus family, were sent by Paula Broadwell. And as they dug deeper, the affair between Broadwell and Petraeus came to light. NBC's Andrea Mitchell reports.
A senior defense official told reporters Tuesday that it was alleged there had been ?inappropriate communications? between Allen and Jill Kelley.
He also said the general ?disputes that he has engaged in any wrongdoing in this matter.??The official said the investigation involved some 20,000 to 30,000 pages, mostly of emails, which were sent from 2010 to 2012.
The Petraeus scandal emerged after Kelley complained to the FBI about receiving anonymous threatening emails.
During the investigation, agents discovered emails between Petraeus and his biographer Paula Broadwell that were indicative of an extramarital affair between them, according to government and law enforcement officials.?
Officials have told NBC News that FBI agents traced the allegedly threatening emails received by Kelley to Broadwell.
Some members of Congress are saying that they or, at the least President Obama, should have been told about the investigation into the director of the CIA while it was going on. NBC's Pete Williams reports.
Petraeus, who was appointed 14 months ago to head the Central Intelligence Agency, announced his resignation on Friday, citing an extramarital affair.
Confirmation hearing on hold
Allen is currently in line to take over as head of U.S. forces in Europe and NATO's Supreme Allied Commander in Europe.
On Monday, he was in Washington, D.C., preparing for his Senate confirmation hearings which were originally scheduled for Thursday, NBC News reported. That nomination has now been put on hold ?until the relevant facts are determined,? Panetta?s statement said.
?The secretary has asked both Senators Levin and McCain that the confirmation hearing on General Allen's pending nomination to be Commander of the United State European Command and Supreme Allied Commander, Europe be delayed,? the statement said.
Allen had no advance warning about the investigation, a close aide of Allen?s told NBC News. He was alerted to the probe by the chairman of the Joint Chiefs of Staff, Gen. Martin Dempsey Monday night ET. Allen had a number of meetings scheduled for Tuesday on Capitol Hill, although the aide was unsure if they would take place.
Allen?s connection to the Petraeus investigation also seems to have caught the Defense Department off guard.
?This came as very surprising news, to say the least. No one in the Pentagon is leaping to conclusions just yet,? a senior defense official traveling with Panetta told NBC News.? ?It's important to review the materials to determine the facts, and it's too early speculate about where this will lead.? In the meantime, Gen. Allen needs to focus on the war effort, which he's successfully led since last year.?
The ISAF was also unaware of the investigation until late Monday or early Tuesday, and it declined to comment, in a written statement, referring all questions to the Defense Department.
Allen, a highly decorated officer, took over as ISAF commander in July 2011, and was nominated?on Oct. 10 to take over as NATO commander, the same time that his successor at the ISAF was named as General Joseph Dunford.
The confirmation of Dunford, currently assistant commandant of the Marine Corps, is now expected to be fast tracked.
?The secretary has respectfully requested that the Senate act promptly on that nomination," Panetta?s statement said.
NBC News' Courtney Kube, Ian Johnston and Rachel Elbaum contributed to this report.
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