WASHINGTON - An FBI investigation that led to the resignation of ex-CIA chief David Petraeus also turned up evidence that General John Allen, the top US commander in Afghanistan, was exchanging potentially ‘inappropriate’ emails with the second woman involved in the scandal, according to American media reports.

Defence Secretary Leon Panetta said in a statement Tuesday that he had ordered an investigation of Allen after the FBI informed the Pentagon it had uncovered thousands of pages of emails between Allen and Jill Kelley, a 37-year old who has been described as an unpaid social liaison at MacDill Air Force Base, Florida, which is headquarters to the US Central Command.

Kelley’s complaints to the FBI that she had received anonymous e-mails warning her to stay away from Gen Petraeus led the FBI to open an investigation that ultimately traced the e-mails to Paula Broadwell, Petraeus’s biographer, who was involved in an affair with Petraeus, The Los Angeles Times reported Tuesday.

One official said that Allen who is married, had denied having an inappropriate relationship with Kelley, who is married to a Tampa doctor and known among officers at Central Command for hosting social events and for forging social ties with top commanders in Tampa.

Officials refused to describe the nature of the emails between Kelley and Allen, who replaced Petraeus as the top commander in Afghanistan and was nominated in October by President Obama to take over as Supreme Allied Commander in Europe, according to the LA Times. Panetta asked the Senate to place Allen nomination on hold until after the investigation is complete.

A spokesman for Allen, who has been in Washington preparing for his confirmation hearings, had no comment on the investigation. Efforts to reach Kelley were also unsuccessful. She was last year given an award for her support to Central Command and was named an honorary ambassador for the command, an unpaid position with no official duties.

But Kelley has angered some senior officers by her persistent efforts to forge close personal ties to successive Central Command four-star officers, by deluging with emails. After being named honourary ambassador, she asked the command for staff at the headquarters to help her organize social functions, a former US official said.

Panetta said that Allen would remain in command in Afghanistan while the investigation into the email by the Defense Department inspector general is conducted.

The FBI’s decision to refer the matter to the Pentagon, along with Panetta’s decision to allow Allen to continue as commander of US and international forces in Afghanistan, suggested that officials viewed the matter as a possible infraction of military rules rather than a violation of federal criminal law.

“His leadership has been instrumental in achieving the significant progress that ISAF, working alongside our Afghan partners, has made in bringing greater security to the Afghan people, Panetta said. “He is entitled to due process in this matter.”

At the same time, Panetta urged the Senate to move ahead on confirmation hearings for Gen Joseph Dunford, the Marine who has been selected by Obama to succeed Allen in Kabul.

Agencies add: The discovery of a trove of correspondence between General John Allen and the woman who led the FBI to Petraeus’s former mistress prompted President Barack Obama to put Allen’s nomination as Nato’s supreme commander on hold.

A defense official said the FBI probe into the affair had uncovered 20,000 to 30,000 pages of correspondence - mainly emails - between General John Allen, the top US commander in Afghanistan, and the woman who led the FBI to Petraeus’s former mistress.

But it remained unclear what allegations Allen faced, and officials declined to comment on whether the Marine general was accused of using his work email to communicate with Kelley or had disclosed any classified information.

In a statement, National Security Council spokesman Tommy Vietor said Allen would remain in his post in Afghanistan but Obama had put off his nomination as Nato’s top military leader pending an internal Pentagon investigation.

Meanwhile, Obama called on the Senate to act quickly to confirm Marine Corps General Joseph Dunford as the next commander of the Nato-led force in Afghanistan, Vietor said.

Nato declined to comment Tuesday on the investigation into its proposed commander, General John Allen who currently heads alliance forces in Afghanistan, in connection with the scandal surrounding CIA chief David Petraeus.

Separately, a senior US military officer told AFP on Tuesday that the sheer volume of emails sent by General John Allen to a Tampa socialite “may be inappropriate” but does not constitute proof of an affair,.

Allen, the US commander in Afghanistan, “strongly denies” having had a relationship with 37-year-old Jill Kelley — a key figure in the scandal that brought down CIA chief David Petraeus — according to the Washington Post.

According to the daily, which cited a senior US official, Allen exchanged “a few hundred emails” with Kelley over the years when he was deputy commander of US Central Command in Tampa, Florida and she was organizing local parties.

In the mails Allen called Kelley “sweetheart,” a common term of endearment in his native Virginia, but the pair did not have a romantic connection, the official told the Post, speaking on condition of anonymity.

But another US officer told AFP the huge extent of the correspondence could have constituted a “violation of military rules” or even “conduct unbecoming of an officer,” which could lead to Allen being sanctioned.

According to the officer cited in the Post report, Broadwell had also sent an anonymous mail to Allen about Kelley. He discussed the mail with Kelley, but did not realize it had come from Broadwell.