Gen. John Allen probed over 'inappropriate' emails

Francois Lenoir / Reuters U.S. General John Allen, commander of the international forces in Afghanistan, seen at NATO headquarters in Brussels Oct. 10, is under investigation over "inappropriate" emails. By Ian Johnston, NBC News 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 a woman who was a key player in the downfall of 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. Kelley complained to the FBI about receiving threatening emails and, during their 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. 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. Officials have also told NBC News that FBI agents traced emails received by Kelley to Broadwell. Allen is currently in line to take over as head of U.S. forces in Europe and NATO's Supreme Allied Commander in Europe. That nomination has been put on hold, Panetta's statement said, "until the relevant facts are determined." "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. "The President has nominated General Joseph Dunford, Assistant Commandant of the Marine Corps, to succeed General Allen at ISAF," it added. "The secretary has respectfully requested that the Senate act promptly on that nomination." More content from NBCNews.com: Source: FBI agent's call didn't affect Petraeus probe Red Cross pushes back on Sandy, calls response 'near flawless' Woman fired over racist anti-Obama Facebook post Obama lays wreath, honors nation's veterans Earthquake rattles eastern Kentucky Video: Sandy victims call ordeal 'a horror movie'