* Defense Secretary asked president to delay general's nomination
* Alleged inappropriate communication involved; Allen denies wrongdoing
* Investigation involves woman at center of Petraeus scandal
* Official says FBI uncovered 20,000-30,000 pages of mostly emails
By Phil Stewart
PERTH, Nov 13 (Reuters) - The top U.S. commander in Afghanistan, General John Allen, is under investigation for alleged inappropriate communication with a woman at the center of the sex scandal involving former CIA Director David Petraeus, a senior U.S. defense official said on Tuesday.
The shocking revelation threatens to fell another of the U.S. military's biggest names and suggests that the scandal involving Petraeus - a retired four-star general who had Allen's job in Afghanistan before moving to the CIA last year - could expand much further than previously imagined.
The U.S. official said the FBI uncovered between 20,000 and 30,000 pages of communications - mostly emails and s panning from 2010 to 2012 - between Allen and Jill Kelley, who has been identified as a long-time friend of the Petraeus family and a Tampa, Florida, volunteer social liaison with military families at MacDill Air Force Base.
It was Kelley's complaints about harassing emails from the woman with whom Petraeus had had an affair, Paula Broadwell, that prompted an FBI investigation, ultimately alerting authorities to Petraeus' involvement with Broadwell. Petraeus resigned from his job on Friday.
It was unclear how Allen knew Kelley, but he was stationed in Tampa as the deputy director of the U.S. military's Central Command for the three years until he took over in Afghanistan in 2011. Petraeus was head of the Tampa-based Central Command from 2008 to 2010.
Asked whether there was concern about the disclosure of classified information, the official, on condition of anonymity, said: "We are concerned about inappropriate communications. We are not going to speculate as to what is contained in these documents."
But even the sheer volume of communication alone could raise questions. Allen and Kelley were exchanging around 30 pages of communication per day, on average. Even if the notes were short, such intense interaction might have consumed a lot of Allen's time.
Defense Secretary Leon Panetta said in a statement given to reporters flying with him to Perth, A ustralia that he had asked that Allen's nomination to be Commander of U.S. European Command and Supreme Allied Commander Europe be delayed "and the president has agreed".
Allen, who is now in Washington, was due to face a Senate confirmation hearing on Thursday, as was his slated successor in Afghanistan, General Joseph Dunford.
The FBI referred the case to the Pentagon on Sunday and Panetta directed the Defense Department's Inspector General to handle its investigation. Panetta informed the top Republican and Democrat on the Senate Armed Services Committee during the overnight flight to Australia. The House Armed Services Committee was also notified.
The U.S. defense official said that Allen denied any wrongdoing and that Panetta had opted to keep him in his job while the matter was under review, and until Dunford can be confirmed to replace him - a process that gains urgency given the potentially lengthy review process and the cloud it could cast over the mission in Afghanistan.
"While the matter is under investigation and before the facts are determined, General Allen will remain commander of ISAF," Panetta said, referring to the NATO-led force in Afghanistan.
Only hours earlier, Panetta had said he was reviewing Allen's recommendations on the future U.S. presence in Afghanistan after most troops withdraw by the end of 2014.
Commending Allen's leadership in Afghanistan, Panetta said in his statement: "He is entitled to due process in this matter."
At the same time, he noted that he wanted the Senate to act "promptly" on Dunford's nomination.
The U.S. official said Panetta was informed of the matter involving Allen on Sunday, as he flew to Hawaii, after the Pentagon's top lawyer called Panetta's chief of staff. The White House was informed next.
FBI RAID, SHIRTLESS PHOTOS
Evidence that the case involving Petraeus was not fully closed came late Monday when FBI agents searched the Charlotte, North Carolina house of Broadwell.
Agents entered the house carrying boxes at around 9 p.m. (0200 GMT Tuesday) and about four hours later took away what appeared to be two computers and about 10 boxes.
During the search, agents inside could be seen moving through multiple rooms, gathering materials and taking photos. They did not comment to reporters gathered outside the house.
Broadwell's family was not at home at the time of the raid. The FBI and a Justice Department official would not comment on the reason for the raid.
U.S. officials had said in recent days that their investigation was largely complete and that prosecutors had determined it was unlikely they would bring charges in that case, which started when Kelley contacted an FBI agent in Tampa about harassing emails from an anonymous source.
That FBI agent, who has not been identified, has also come under scrutiny after it was discovered he had sent shirtless photographs of himself to Kelley, but "long before" this investigation, a law enforcement official told Reuters. The photographs were first reported by the Wall Street Journal.
The agent had never been on the Broadwell case, but had taken the information about the emails to the FBI cyber squad in Tampa, the law enforcement official said.
The FBI agent who works in the Tampa office apparently became frustrated at the pace of the investigation and complained to a member of Congress about it, the official said.
The FBI investigation of the emails received by Kelley traced them to Broadwell and subsequently uncovered emails that revealed an affair between Broadwell and Petraeus.
The emails between the two women were of a "childish", jealous nature and showed some one-upmanship of trying to come across as being more important to Petraeus, the official said.
When Petraeus resigned as CIA director on Friday he publicly admitted to having engaged in an extramarital affair.
Lawmakers and others have questioned whether Broadwell, who co-wrote a biography of the decorated former general, obtained classified information from him or another source.
Panetta had earlier said Petraeus did the right thing by stepping down, given potential security concerns, even as he said he was saddened by the end of the retired general's distinguished career.