General John R. Allen, a second top military official, was dragged in to the David Petraeus sex scandal early this morning after being accused of sending thousands of “inappropriate” emails to socialite Jill Kelley, who was responsible for exposing the former CIA director’s extra-marital affair.

General John R. Allen, commander of U.S. and NATO troops in Afghanistan, is under investigation by the FBI after the agency discovered between 20,000 and 30,000 pages of communication between him and 37-year-old housewife Jill Kelley.

Jill Kelley entered the public eye when she was the target of threatening emails from Paula Broadwell, which the FBI used to uncover the affair between Broadwell and David Petraeus, leading to the former general’s resignation from the CIA.

John Allen, who succeeded David Petraeus in Afghanistan, was due to take over as NATO’s top commander, but his appointment has been suspended while his relationship with Jill Kelley is investigated.

Barack Obama had nominated John Allen to take over as chief of the military’s European Command and NATO’s Supreme Allied Commander in Europe, but that nomination is now on hold as the Pentagon investigates Allen’s relationship with Kelley, Defense Secretary Leon Panetta told reporters.

He had been expected to take that new post in early 2013 if confirmed by the Senate, as had been widely expected.

The FBI notified the Pentagon of its investigation into John Allen’s communications with Jill Kelley on Sunday evening, an unnamed senior defence official said. Leon Panetta said he immediately notified the White House and top leaders in Congress of the investigation.

Leon Panetta said John Allen would remain as commander of U.S. and NATO forces in Afghanistan for now, “while the matter is under investigation and before the facts are determined”.

Pentagon officials have declined to comment on the nature of the relationship between Jill Kelley and John Allen, who is married, except to say that it was “potentially inappropriate”. Officials have not said whether any national security secrets were breached.

Adultery is classified as a crime in the military.

Jill Kelley has been in the news this week after it emerged that she was the target of harassing emails from Paula Broadwell, a 40-year-old mother of two from Charlotte, North Carolina who was engaged in an affair with David Petraeus.

Paula Broadwell sent Jill Kelley a half dozen emails from anonymous accounts earlier this year warning her to stay away from Petraeus. Paula Broadwell perceived Jill Kelley as a threat to her relationship with David Petraeus, which began in the summer of 2011 and ended the following summer.

Jill Kelley notified a friend of hers who worked for the FBI of the emails, and he referred the case to a cyber crimes unit.

That agent was later banned from the FBI’s investigation into the source of the emails when officials discovered that he was sending shirtless photographs to Jill Kelley and seemed to become “obsessed” with the case, the Wall Street Journal reported.

General John R. Allen was dragged into the David Petraeus sex scandal early this morning after being accused of sending thousands of inappropriate emails to Jill Kelley

Jill Kelley is a volunteer who organizes social events for military families in the Tampa area. She often hosts the events at her million-dollar Bayshore Boulevard home, which is located only a couple miles from MacDill Air Force base, where Allen served from July 2008 to June 2011.

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

A senior official told the Associated Press that 20,000 to 30,000 pages of emails and other documents from Allen’s communications with Jill Kelley between 2010 and 2012 are under review.

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 David Petraeus is mentioned in the emails.

“General Allen disputes that he has engaged in any wrongdoing in this matter,” the official said. He said John Allen currently is in Washington.

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

John Allen was Deputy Commander of Central Command, based in Tampa, prior to taking over in Afghanistan. He also is a veteran of the Iraq war.

Leon Panetta said Barack Obama was consulted and agreed that John Allen’s nomination to the NATO post should be put on hold.

John Allen was to testify at his confirmation hearing before the Senate Armed Services Committee on Thursday. Leon Panetta said he asked committee leaders to delay that hearing.

Leon Panetta also said he wants the Senate Armed Services Committee to act promptly on Barack Obama’s nomination of General Joseph Dunford to succeed John Allen as commander in Afghanistan. That nomination was made several weeks ago. Joseph Dunford’s hearing is also scheduled for Thursday.