WASHINGTON — A Pentagon investigation has cleared Gen. John Allen, the top U.S. commander in Afghanistan, of professional misconduct in exchanging emails with a civilian woman linked to the sex scandal that led retired Gen. David Petraeus to resign as CIA director.

Pentagon press secretary George Little said Tuesday that Defense Secretary Leon Panetta was informed of the conclusion by the Pentagon's inspector general.

"The secretary was pleased to learn that allegations of professional misconduct were not substantiated by the investigation," Little said, adding that Panetta has "complete confidence in the continued leadership" of Allen.

The matter had been referred to the Pentagon in November by the FBI during the course of its investigation of emails between Petraeus and his biographer-turned-paramour, Paula Broadwell. The FBI turned up thousands of emails between Allen and Jill Kelley, who was said to have received threatening emails from Broadwell.

At the time, officials said 20,000 to 30,000 pages of emails and other documents from Allen's communications with Kelley between 2010 and 2012 were in question. None of the emails have been made public.

Shortly after being contacted by the FBI, Panetta referred the matter to the Pentagon's inspector general, while expressing confidence in Allen and deciding that he would remain in Kabul as commander of all allied forces in Afghanistan.

At the same time, Allen's nomination to be the next U.S. commander of NATO forces in Europe was put on hold. The officials said Tuesday the White House had not decided whether to go forward with the nomination.

Maj. David Nevers, a spokesman for Allen, said he had no immediate comment on reports of his being exonerated.

Allen's successor in Kabul, Marine Gen. Joseph Dunford, has been confirmed by the Senate and is scheduled to take over on Feb. 10.

Allen had maintained he did nothing wrong in the Kelley communications, but he has not spoken publicly about the specifics of his email exchanges with her. She served as a sort of social ambassador for U.S. Central Command in Tampa, Fla.

Petraeus is a former Central Command commander, and Allen is a former deputy commander there.

Shortly after he referred the emails to the inspector general, Panetta asked the Joint Chiefs of Staff to review ethics training and to brainstorm on ways to steer officers away from trouble. The move was a reflection of the depth of concern triggered by a series of misconduct cases in a military that prides itself on integrity and honor.

Gen. Martin Dempsey, chairman of the Joint Chiefs, has not released the results of his review but has said he found that ethics training for senior leaders, while adequate, should begin earlier in an officer's career and be reinforced more frequently.

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  • David Petraeus

    A highly decorated four-star Army general lauded for his leadership of the Iraq and Afghanistan wars, Petraeus moved into the civilian world to become CIA director in September 2011. He shocked official Washington on November 9, 2012 by admitting an extramarital affair with his biographer and resigning his spymaster post. (Text via <a href="http://www.huffingtonpost.com/huff-wires/20121114/us-scandal-scorecard/">The Associated Press</a>)

  • Paula Broadwell

    The other woman. An author and married mom of two young children, she was a West Point-educated Army reservist and graduate student when she met Petraeus at Harvard in 2006. She later embarked on a case study on his leadership of the Iraq War. After he took the helm in Afghanistan, Broadwell expanded her work into a biography, gaining unprecedented access to Petraeus and his commanders. It's called "All In: The Education of General David Petraeus." Their affair began in November 2011, a couple of months after he became CIA director, according to retired Army Col. Steve Boylan, a friend of the Petraeus family. It ended last summer, Boylan said. The relationship was exposed after Broadwell of Charlotte, N.C., sent emails to another woman, Jill Kelley, warning her to stay away from Petraeus, officials said. (Text via <a href="http://www.huffingtonpost.com/huff-wires/20121114/us-scandal-scorecard/">The Associated Press</a>)

  • Jill Kelley

    All threads in the story trace back to this Tampa, Fla., socialite. A surgeon's wife and mother of three children, Kelley is a sort of self-appointed social ambassador for the nearby U.S. Central Command and other officers at MacDill Air Force Base. The Kelleys opened their bayside home to lavish parties where military brass mingled with Tampa's elite. In this role, she befriended Petraeus and his wife, Holly, when he took over Central Command in October 2008. Kelley stayed in close contact with Petraeus after he left to take command of the Afghanistan war. They exchanged nearly daily emails in an account routinely monitored by his aides, according to two former staffers, who said those messages weren't romantic in tone. In May 2012, Kelley started getting anonymous, harassing emails warning her away from Petraeus. She reported the email to the FBI. The FBI traced the messages to Broadwell, uncovering her affair with Petraeus. The FBI notified Petraeus' boss, Director of National Intelligence James Clapper, who urged him to resign. And the FBI found something more. It unearthed "inappropriate communications" between Kelley and another top military officer, John Allen, according to Pentagon officials. (Text via <a href="http://www.huffingtonpost.com/huff-wires/20121114/us-scandal-scorecard/">The Associated Press</a>)

  • John Allen

    The four-star Marine general who followed in Petraeus' footsteps at Central Command and then as top U.S. commander in Afghanistan is now following him into choppy waters. The Pentagon is investigating 20,000 pages of documents and emails involving Allen, who is married, and Kelley. Some of the communications were "flirtatious," according to a senior defense official, who spoke on condition of anonymity because he wasn't authorized to discuss the case publicly. Like Petraeus, Allen, 58, was part of the Tampa social circle; he moved up to acting commander when Petraeus left for Afghanistan. When Petraeus came home from Afghanistan, Allen moved into the top job there – his current post. President Barack Obama had nominated Allen to take over U.S. European Command and lead all NATO forces in Europe. (Text via <a href="http://www.huffingtonpost.com/huff-wires/20121114/us-scandal-scorecard/">The Associated Press</a>)

  • Natalie Khawam

    Kelley's twin sister also socialized with the two generals. Both Petraeus and Allen wrote letters lauding Khawam as a devoted mother to help her in a bitter child custody battle with her ex-husband. Earlier in that divorce case, Superior Court Judge Neal Kravitz had criticized Khawam for a lack of honesty and "misrepresentations about virtually everything." (Text via <a href="http://www.huffingtonpost.com/huff-wires/20121114/us-scandal-scorecard/">The Associated Press</a>)

  • Holly Petraeus

    Petraeus' wife of 38 years, mother of their two grown children, is in charge of service member assistance at the Consumer Financial Protection Bureau and is a well-known advocate for military families. Mrs. Petraeus is said to be devastated by her husband's infidelity. "Furious would be an understatement," family friend Boylan told ABC's "Good Morning America." (Text via <a href="http://www.huffingtonpost.com/huff-wires/20121114/us-scandal-scorecard/">The Associated Press</a>)

  • FBI Agent Frederick W. Humphries

    Humphries, 47, was the agent who initially saw the emails the FBI said Petraeus' biographer and mistress, Paula Broadwell, sent to Tampa socialite Jill Kelley, a woman she apparently saw as a rival for Petraeus' affections. She also allegedly sent emails to Gen. John Allen, Kelley's friend and the top U.S. commander in Afghanistan. Concerned about the emails, Kelley contacted Humphries in June. The two had met at a 2011 FBI Citizens Academy, a program aimed at teaching the public and journalists about what the agency does and how it operates. Kelley was in the class, which Humphries lectured one night about terrorism, according to Natalie Shepherd, a Tampa TV reporter who was there. Humphries, a former Army captain who worked in military intelligence, thought the emails raised serious concerns because the anonymous author knew the comings and goings of Allen and Petraeus, a former general who had preceded Allen in Afghanistan. His report back to the FBI started the investigation that led to Broadwell and uncovered her affair with Petraeus. (Text via <a href="http://www.huffingtonpost.com/2012/11/14/frederick-humphries_n_2134203.html" target="_hplink">The Associated Press</a>)