WASHINGTON — Conflicting portrayals of e-mails written by Gen. John R. Allen, the top American and NATO commander in Afghanistan, emerged Tuesday after it was disclosed that the general was under investigation for what the Pentagon called “inappropriate communication” with the woman whose complaint to the F.B.I. set off the scandal involving David H. Petraeus’s extramarital affair.
Defense Secretary Leon E. Panetta and other officials traveling with him to Australia overnight on Monday disclosed the inquiry into General Allen’s e-mails with Jill Kelley, the woman in Tampa, Fla., who was seen by Paula Broadwell, Mr. Petraeus’s lover, as a rival for his attentions.
Mr. Panetta, along with Gen. Martin E. Dempsey, the chairman of the Joint Chiefs of Staff, referred the Allen matter to the Pentagon’s inspector general, according to Mr. Panetta’s aides, after a team of military and civilian lawyers reviewed what defense officials say are thousands of pages of documents, including hundreds of e-mails between General Allen and Ms. Kelley, that the F.B.I. forwarded to the Pentagon.
Associates of General Allen said Tuesday that the e-mails were innocuous. Some of them used terms of endearment, but not in a flirtatious way, the associates said. “If you know Allen, he’s just the kind of guy to respond dutifully to every e-mail he gets — ‘you’re the best,’ ‘you’re a sweetheart,’ that kind of thing,” according to a senior American official who is familiar with the investigation.
Even so, other Pentagon officials briefed on the content of the e-mails said that some of the language did, on initial reading, seem “overly flirtatious” and warranted further inquiry.
The Pentagon’s top lawyer, Jeh Johnson, recommended sending the matter to the inspector general, senior defense officials said. An inappropriate communication could violate military rules.
Senior officials in the Obama administration and lawmakers from both parties expressed shock at what could be a widening scandal into two of the most prominent generals of their generation: Mr. Petraeus, who was the top commander in Iraq and Afghanistan before he retired from the military to become director of the C.I.A., only to resign on Friday because of his affair, and General Allen, who also served in Iraq and now commands 68,000 American troops in Afghanistan.
President Obama, however, voiced support for General Allen through his spokesman on Tuesday. “The president thinks very highly of General Allen,” the spokesman, Jay Carney, said at a White House news briefing. “He has faith in General Allen.”
But the matter has created enough concern that General Allen’s recent nomination to become NATO’s top military officer was delayed at Mr. Panetta’s request, pending the investigation’s outcome.
Aides traveling with Mr. Panetta, reacting to anger from some of General Allen’s associates who said he was being unfairly treated, described Mr. Panetta as having great respect for General Allen. But they said that Mr. Panetta had little choice in referring the matter to the inspector general. General Dempsey informed General Allen of the investigation on Monday from Perth, where he had traveled for a security meeting that Mr. Panetta is also attending.
General Allen, a Marine, succeeded Mr. Petraeus as the top allied commander in Afghanistan in July 2011. He also served as Mr. Petraeus’s deputy when both officers led the military’s Central Command, based in Tampa, from 2008 until 2010.
General Allen’s connection to the scandal appears to have originated with an e-mail he received from an account that was registered under a fake name and has now been linked to Ms. Broadwell, according to a senior American official. The e-mail warned General Allen to be wary of Ms. Kelley and was vaguely threatening. Though he did not know who had written the e-mail, he was concerned and passed it on to Ms. Kelley. She then discussed it with an agent she knew at the F.B.I.’s field office in Tampa, whose cybercrime unit opened an investigation that eventually linked Ms. Broadwell to General Petraeus.
A senior law enforcement official in Washington said Tuesday that F.B.I. investigators, looking into Ms. Kelley’s complaint about anonymous e-mails she had received, examined all of her e-mails as a routine step. Officials familiar with the investigation said it covers 20,000 to 30,000 page of documents, but Pentagon officials cautioned against making too much of that number, since some might be from e-mail chains, or brief messages printed out on a whole page.
On Monday night, F.B.I. agents searched Ms. Broadwell’s home in Charlotte, N.C., and local television news crews filmed them carrying away boxes of material in what officials said was part of that continuing investigation.
The defense official said that the e-mails between Ms. Kelley and General Allen spanned the years 2010 to 2012.
American officials familiar with the social dynamics at the upper echelons of the Central Command described Ms. Kelley as wealthy socialite who knew “almost every” high-ranking officer serving in Tampa. Her ties were close enough that Mr. Petraeus and General Allen both intervened last September in a messy custody dispute on behalf of Ms. Kelley’s twin sister, Natalie Khawam.
A senior official said Ms. Kelley was close to both General Allen and his wife. She would often send e-mails, hundreds over the course of any given year, to the couple about parties or people she had met or trips she was considering. General Allen was never alone with Ms. Kelley, the official said, and while he may have been “affectionate in a few e-mails with her, there’s nothing he’s embarrassed about or embarrassed to tell his wife about.”
