Second top general in Petraeus probe

The Petraeus investigation has expanded to include General John Allen, the top US commander in Afghanistan. Source: AP

THE top American commander in Afghanistan, General John Allen, is under investigation for alleged "inappropriate communications" with a woman said to have received threatening emails from Paula Broadwell, the woman with whom General David Petraeus had an affair.

Even as the FBI prepared a timeline of its investigation that brought to light David Petraeus' extramarital affair, Defence Secretary Leon Panetta revealed that the Pentagon had begun an internal investigation into thousands of pages of emails from Gen John Allen to a second woman involved in the Petraeus case.

Allen succeeded Petraeus as the top American commander in Afghanistan in July 2011, and his nomination to become the next commander of U.S. European Command and the commander of NATO forces in Europe has now been put on hold.

US Defence Secretary Leon Panetta said in a written statement issued to reporters aboard his aircraft, en route from Honolulu to Perth, that the FBI referred the matter to the Pentagon on Sunday.

Panetta said that he ordered a Pentagon investigation of Allen on Monday.

 General John Allen, the top American commander in Afghanistan, is under investigation for alleged "inappropriate communications'' with Jill Kelley.

A senior defence official travelling with Panetta said Allen's communications were with Jill Kelley, who has been described as an unpaid social liaison at MacDill Air Force Base, Florida., which is headquarters to the U.S. Central Command. She is not a U.S. government employee.

A Pentagon official said 20,000 to 30,000 pages of emails and other documents from Allen's communications with Kelley between 2010 and 2012 are under review. He would not say whether they involved sexual matters or whether they are thought to include unauthorised disclosures of classified information. He said he did not know whether Petraeus is mentioned in the emails.

Allen has denied any wrongdoing.

Ms Kelley is said to have received threatening emails from Paula Broadwell, the woman with whom former CIA Director David Petraeus had an extramarital affair.

FBI agents carry boxes and a computer from the home of Paula Broadwell, whose affair with retired Gen David Petraeus led to his resignation as CIA director. Picture: AP

Meanwhile, FBI agents have searched the home of Broadwell, Petraeus' biographer. It was Broadwell's threatening emails to Jill Kelley, a Florida woman who is a Petraeus family friend, that led to the FBI's discovery of communications between Broadwell and Petraeus indicating they were having an affair.

The Petraeus scandal, with its allegations of "catty" emails and secret trysts, has rocked Washington.

In one particularly bizarre twist, the FBI agent assigned to the case is understood to have been stood down after reportedly sending Ms Kelley shirtless pictures of himself.

Petraeus resigned as CIA director on Friday.

The FBI uncovered the affair between CIA chief David Petraeus and Paula Broadwell while investigating threatening emails sent to Jill Kelley.

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

The senior official, who discussed the matter only on condition of anonymity because it is under investigation, said Panetta believed it was prudent to launch a Pentagon investigation, although the official would not explain the nature of Allen's problematic communications.

Panetta said that while the matter is being investigated by the Defence Department Inspector General, Allen will remain in his post as commander of the International Security Assistance Force, based in Kabul. He praised Allen as having been instrumental in making progress in the war.

In a White House statement early Tuesday, National Security spokesman Tommy Vietor said President Barack Obama has held Allen's nomination at Panetta's request. Obama, the statement said, "remains focused on fully supporting our extraordinary troops and coalition partners in Afghanistan, who Gen Allen continues to lead as he has so ably done for over a year."

A Florida woman Jill Kelley has allegedly received harassing emails from Paula Broadwell that led federal investigators to discover David Petraeus's sexual indiscretion. Source: Fox News

But the Allen investigation adds a new complication to an Afghan war effort that is at a particularly difficult juncture. Allen had just provided Panetta with options for how many US troops to keep in Afghanistan after the U.S.-led coalition's combat mission ends in 2014. And he was due to give Panetta a recommendation soon on the pace of U.S. troop withdrawals in 2013.

The war has been largely stalemated, with little prospect of serious peace negotiations with the Taliban and questions about the Afghan government's ability to handle its own security after 2014.

At a photo session with Australian Prime Minister Julia Gillard shortly after he arrived in Perth, Panetta was asked by a reporter whether Allen could remain an effective commander in Kabul while under investigation. Panetta did not respond.

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 strongly that officials viewed whatever happened as a possible infraction of military rules rather than a violation of federal criminal law.

CIA Director David Petraeus has resigned from his post, citing an extramarital affair.

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.

In the meantime, 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.

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

The senior defense official said Panetta has not talked to Allen about the investigation, nor has he discussed the matter with President Barack Obama, although he consulted with unspecified White House officials before making the decision to seek a postponement of Allen's confirmation hearing.

Panetta did talk about the Allen matter with General Martin Dempsey, chairman of the Joint Chiefs of Staff, who happens to also be in Perth for a meeting of American and Australian diplomatic and defence officials.

With a cloud over Allen's head, it was unclear whether he would return to Kabul, even though Panetta said Allen would remain in command. The second-ranking American general in Afghanistan is Army Lt. Gen. James Terry.

NATO officials had no comment about the delay in Allen's appointment.

"We have seen Secretary Panetta's statement," NATO spokeswoman Carmen Romero said in Brussels. "It is a U.S. investigation."

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

In yet another twist, the FBI agent assigned to the case is understood to have been stood down after reportedly sending Ms Kelley shirtless pictures of himself.

Earlier today, the scandal widened with revelations that the federal agent who launched the investigation was barred from taking part in the case after allegedly sending shirtless photos of himself to Jill Kelley, the Wall Street Journal reports. 

Supervisors reportedly removed the agent from the case over concerns that he was becoming obsessed with the case.

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