By Luke Harding, The Guardian

Defence secretary Leon Panetta confirms FBI is investigating US commander over his 'inappropriate' emails with Florida woman

The scandal involving former CIA director David Petraeus has deepened following allegations that another top US military commander, General John Allen, had sent thousands of "inappropriate" emails to a woman linked to Petraeus.

The US defence secretary, Leon Panetta, confirmed on Tuesday the FBI was investigating Allen, the US's leading commander in Afghanistan, over his "communications" with a Florida woman, Jill Kelley. Petraeus resigned on Friday over an affair with his biographer Paula Broadwell. The affair had come to light after Kelley complained of "harassing" emails traced back by the FBI to Broadwell.

In a statement, Panetta said the FBI on Sunday referred "a matter involving" General Allen to the Pentagon. The Pentagon's inspector general was examining 20,000 to 30,000 pages of documents, including many emails between Allen and Kelley. Officials quoted by the New York Times said there was a "distinct possibility" the emails were connected to the FBI's investigation into Petraeus.

The widening scandal is an embarrassment for President Obama and has engulfed his national security command, with the CIA, FBI, Pentagon and military all now involved.

Petraeus is a former four-star general who had Allen's job in Afghanistan before moving to the CIA last year. Allen, who also served in Iraq, is in charge of the US's 68,000 troops in Afghanistan and recently submitted proposals on the US's military presence i after 2014 when most US soldiers pull out. Obama was due to nominate Allen to become the commander of American forces in Europe and the supreme commander of Nato, with the Senate expected to confirm both positions.

Speaking on his plane en route to Australia, Panetta said he had recommended Allen nomination be put on hold – adding that the president had "agreed".

In a statement, the US defence secretary praised Allen for his leadership in Afghanistan and said he was "entitled to due process in this matter", the NYT reported. Allen would remain commander of Isaf, the international security assistance force in Afghanistan, Panetta said, adding he wanted the Senate to swifly confirm assistant Marine Corps commandant Joseph Dunford, as Allen's successor.

The "inappropriate" emails between Allen and Kelley date from 2010 to 2012. Kelley is a long-time friend of the Petraeus family and a volunteer social liaison in Tampa, Florida, with military families at MacDill air force base. She has so far not commented on the allegations.

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."

On Monday night, FBI agents trawled through Broadwell's home in Charlotte, North Carolina. Agents entered the house carrying boxes and about four hours later took away what appeared to be two computers and about 10 boxes. During the search, agents could be seen moving through 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.

The imbroglio at the top of the US army grew even more bizarre after it emerged that one of the FBI agents involved in the case had sent shirtless photographs of himself to Kelley. The photos were sent "long before" the investigation into Petraeus began, a law enforcement official told Reuters. The Wall Street Journal on Tuesday reported that Kelley had approached the agent after receiving anonymous harassing emails.

The federal agent, a friend of Kelley's, referred the emails to a cyber crimes unit, which began an investigation. According to the WSJ, his superiors grew increasingly concerned and concluded the agent had become obsessed with the matter. Some reports suggest the agent was taken off the investigation, while others said he had never been assigned to the Broadwell case.

Either way, the agent grew frustrated at the pace of the investigation and contacted a member of Congress, Republican David Reichert, officials said. Reichert appears to have relayed the agent's concerns to the FBI's headquarters in Washington. The FBI by this time had established that Broadwell was the author of the harasssing emails, and had stumbled upon evidence that Petraeus and Broadwell were having an affair.

Broadwell used several anonymous email accounts she shared with her husband to send the accusing emails, officials said. The emails between the two women were of a "childish", jealous nature and showed some oneupmanship of trying to come across as being more emotionally important to Petraeus. In one email, Broadwell claimed she had watched Kelley touch "him" [Petraeus] provocatively under the table, officials added.

Petraeus and Broadwell communicated with each other using private Gmail accounts, the FBI revealed. 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. Following several months of investigation, which intensified in early summer, the FBI concluded there had been no national security breach.

Panetta said earlier saidPetraeus did the right thing by stepping down, given potential security concerns, while admitting he was saddened by the end of the retired general's distinguished career.

© Guardian News and Media 2012

[General John Allen via isafmedia /Flickr]