"The secretary was pleased to learn that allegations of professional misconduct were not substantiated by the investigation," Little said, adding that Panetta has "complete confidence in the continued leadership" of Allen.
The matter had been referred to the Pentagon in November by the FBI during the course of its investigation of emails between Petraeus and his biographer-turned-paramour, Paula Broadwell. The FBI turned up thousands of emails between Allen and Jill Kelley, who was said to have received threatening emails from Broadwell.
At the time, officials said 20,000 to 30,000 pages of emails and other documents from Allen's communications with Kelley between 2010 and 2012 were in question. None of the emails have been made public.
Shortly after being contacted by the FBI, Panetta referred the matter to the Pentagon's inspector general, while expressing confidence in Allen and deciding that he would remain in Kabul as commander of all allied forces in Afghanistan.
At the same time, Allen's nomination to be the next U.S. commander of NATO forces in Europe was put on hold. The officials said Tuesday the White House had not decided whether to go forward with the nomination.
Maj. David Nevers, a spokesman for Allen, said he had no immediate comment on reports of his being exonerated.
Allen's successor in Kabul, Marine Gen. Joseph Dunford, has been confirmed by the Senate and is scheduled to take over on Feb. 10.
Allen had maintained he did nothing wrong in the Kelley communications, but he has not spoken publicly about the specifics of his email exchanges with her. She served as a sort of social ambassador for U.S. Central Command in Tampa, Fla.
Petraeus is a former Central Command commander, and Allen is a former deputy commander there.
Shortly after he referred the emails to the inspector general, Panetta asked the Joint Chiefs of Staff to review ethics training and to brainstorm on ways to steer officers away from trouble. The move was a reflection of the depth of concern triggered by a series of misconduct cases in a military that prides itself on integrity and honor.
Gen. Martin Dempsey, chairman of the Joint Chiefs, has not released the results of his review but has said he found that ethics training for senior leaders, while adequate, should begin earlier in an officer's career and be reinforced more frequently.