Panetta ordered the inspector general investigation in November after the FBI provided the Pentagon with what officials said were voluminous emails between Allen and Kelley. At the time, Pentagon officials characterized the emails as "potentially inappropriate" and in some cases "flirtatious," but they refused to disclose the contents.
Investigators focused on about 60 to 70 emails, according to one official, who said that some of the language was "perhaps overly familiar" but not inappropriate.
Allen, who is married to a Tampa doctor, and Kelley both denied having an improper relationship, but the investigation led the White House to put on hold plans to nominate him to be supreme allied commander in Europe, the senior military officer at NATO.
The White House has not decided whether the nomination will proceed. Allen is stepping down as commander in Afghanistan next month, and if not nominated for another four-star command, would have to retire.
The messages came to light last year during an FBI investigation that revealed that Petraeus and his biographer, Paula Broadwell, were having an affair. Kelley, who threw parties for Petraeus and other top officers when they were assigned to U.S. Central Command headquarters in Tampa, had gone to the FBI after receiving harassing emails.
The FBI concluded that Broadwell had sent the anonymous emails to Kelley, for reasons that remain unclear. The affair led Petraeus to resign as CIA director in November.
Kelley is known among officers at Central Command for hosting social events and for forging social ties with top commanders in Tampa. Allen was deputy head of Central Command before taking command in Afghanistan last year.
Kelley said in an interview published Tuesday on the Daily Beast website that the emails from Broadwell contained threats, blackmail and extortion demands but that they did not warn her to stay away from Petraeus, as has been previously reported.
Also on Tuesday, Kelley and her husband, Scott, wrote in the Washington Post that they were "surprised to read that Jill had flown on private military jets (never); that she was a volunteer social planner (wrong); that we were suffering financially (false); and, most painful of all because of the innuendo surrounding the allegation, that some 30,000 e-mails were sent to a general from the e-mail address we share. This is untrue, and the insinuation that Jill was involved in an extramarital affair is as preposterous as it is hurtful to our family. This small sample of junk reporting was emotionally exhausting and damaging - as it would be to the strongest of families."
- Daily News wire services