WASHINGTON: The Pentagon has cleared the top US commander in Afghanistan of wrongdoing over emails with a woman tied to the scandal that forced Central Intelligence Agency (CIA) director David Petraeus to resign, a US official said on Tuesday.

The Defence Department's inspector general completely exonerated General John Allen, the outgoing chief of US-led forces in Afghanistan, over the emails, paving the way for his pending nomination to take up command of Nato forces in Europe, the official said.

“Allen has been cleared by the IG,” the official told AFP on condition of anonymity.

The FBI came upon the emails from Allen in its probe of Petraeus, and defence officials had said the tone of the messages had been potentially “inappropriate” and possibly violated rules applying to military officers.

Allen had exchanged messages with Jill Kelley, a Florida socialite who had thrown parties for senior officers at the US Central Command, which has its headquarters in Tampa.

Kelley had alerted the Federal Bureau of Investigation (FBI) to anonymous emails she received and which she claimed were threatening. The emails were traced to David Petraeus's biographer, Paula Broadwell, and authorities then uncovered evidence that Broadwell was having an affair with the CIA director.

The scandal prompted Petraeus to resign abruptly in November from his CIA post, ending a storied career marked by his tenure as military commander in the wars in Iraq and Afghanistan.

But the FBI also found numerous emails between Allen and Kelley, and Defense Secretary Leon Panetta ordered an independent inquiry by the Pentagon inspector general.

Panetta “was pleased to learn that allegations of professional misconduct were not substantiated by the investigation,” and has “complete confidence” in Allen's leadership, his spokesman George Little said in a statement.

Initially, officials had said there were 25,000 to 30,000 pages of correspondence between Allen and Kelley, raising questions that his emails could reflect a distracted commander.

But officials later said the inquiry was only focused on a few hundred messages.

The scandal broke after Allen was nominated to take over as Nato's supreme allied commander, and his confirmation hearings before the US Senate were put on hold as a result.

Throughout the inspector general's inquiry, Panetta and other top officials have expressed full confidence in Allen's handling of the war effort in Afghanistan.

Kelley, in her first interview since the case came to light, said on Tuesday that the media frenzy over the scandal had been a nightmare for her family, that she never had a romantic link to Allen and that she decided not to press charges against Petraeus's mistress over her allegedly menacing messages.

In the emails sent by Broadwell, “there was blackmail, extortion, threats,”Kelley told The Daily Beast. “I knew I was being stalked.”

She and her husband Scott, a surgical oncologist, wrote in a Washington Post op-ed that the invasion of privacy they experienced as a result of the Petraeus affair coming to light was “emotionally exhausting and damaging”.

Allen succeeded Petraeus as the top commander in Afghanistan, taking over in July 2011. The four-star general is due to hand over his post to General Joseph Dunford next month.