The Defense Department’s inspector general has found that allegations that Gen. John Allen engaged in inappropriate behavior in emails he exchanged with Tampa, Fla., socialite Jill Kelley were unsubstantiated. 

"The IG cleared him," a defense official told NBC News, speaking on condition of anonymity. 

Allen, the current commander of NATO forces in Afghanistan, has been nominated to be Supreme Allied Commander in Europe, but that promotion was put on hold when the IG investigation began. The defense official stressed that no decision has been made yet on whether his nomination will go forward again. 

A statement Wednesday by the International Security Assistance Force in Afghanistan on behalf of Allen said he had been informed that investigators  “the allegations against him were unsubstantiated and … that he did not violate the requirement of exemplary conduct or the prohibition against conduct unbecoming an officer and a gentleman. “

“He's obviously pleased by the outcome,” it said. “But more critically, he is grateful for the support he received throughout this process from his chain of command, friends, family and colleagues.  He remains focused, as he has always been, on leading the brave men and women of the ISAF team."

Allen’s nomination was jeopardized  in mid-November when it was revealed that he had exchanged emails with Kelley that some Pentagon officials at the time characterized as “inappropriate” and “flirtatious.” 

Allen had met Kelley when he was commander of MacDill Air Force Base outside Tampa, where she served as a volunteer “social liaison.” 

She inadvertently drew him into the scandal that led to the resignation of former CIA Director David Petraeus by complaining to an FBI agent with whom she was acquainted about anonymous emails referencing Petraeus. Among those emails was one that Allen had forwarded to her in the belief that she had sent it to him as a joke, officials told NBC News at the time. 

FBI agents eventually traced the allegedly threatening emails to Paula Broadwell, Petraeus' biographer. That investigation also led to evidence of an extramarital affair between Petraeus and Broadwell, prompting his resignation on Nov. 7. Days later, Defense Secretary Leon Panetta announced the investigation into Allen’s relationship with Kelley. 

Jill Kelley speaks out: 'I knew I was being stalked'

The inspector general’s investigation does not determine guilt or innocence. Rather, it decides whether an allegation is substantiated or not. Even if the finding is that the allegation is unsubstantiated, the IG can still make a recommendation that can harm an officer’s career. 

Jim Miklaszewski is NBC News' Chief Pentagon Correspondent; Courtney Kube is an NBC News producer at the Pentagon. Mike Brunker, NBC News investigations editor, contributed to this report.

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At least one anonymous email sent to Gen. John Allen, commander of U.S. and NATO forces in Afghanistan, was among those turned over by Tampa, Fla., socialite Jill Kelley to the FBI in June, a senior law enforcement official and a source close to Kelley tell NBC News. Kelley’s complaint to an FBI agent with whom she was acquainted triggered the investigation that ultimately led to the resignation of CIA Director David Petraeus.

The law enforcement official, who spoke on condition of anonymity, said Wednesday that Kelley turned over fewer than a dozen emails to the FBI agent, including at least one that Allen had received and forwarded to her.  The emails were ultimately traced to Paula Broadwell, Petraeus’ biographer and the woman with whom he had an extramarital affair, multiple government and law enforcement officials have told NBC News.

The official said it is not clear who received email from Broadwell first -- Kelley or Allen – but a person close to Kelley told NBC News on Wednesday that Allen received the first email in mid-May. According to the source, who also spoke on condition of anonymity, the email sent from an account called "kellypatrol" said , in essence, “Beware of Jill Kelley. She's the kind of person who could ruin you.” It also referred to a meeting Kelley and her husband were planning in Washington with Allen, the source said.

Allen forwarded the e-mail to Kelley, thinking it was a joke from her. She replied that she hadn’t sent it, the source said.

The law enforcement official said Allen also forwarded the email to a “military authority” within the Department of Defense. The official did not specify which office or individual was notified.

Kelley herself began receiving similar emails in early June, the source close to her said, sent from four or five alias accounts. They contained words to the effect of, “What kind of person are you.” And passages directed to her husband, asked, in essence, “Do you know what your wife is up to?” the source said.

As reported previously by NBC News, Kelley took the emails – including at least one from Allen – to the FBI agent she knew because they made reference to meetings she had planned with both Allen and Petraeus, the source said. Kelley wondered why an anonymous e-mailer would know that kind of detail and became concerned that someone was cyberstalking her or hacking into her e-mails, the person said.

Federal officials confirmed Wednesday that the agent who first took the complaint from Kelley is Frederick Humphries, a counter-terrorism agent who worked on the millennium bomb plot case. His name was first revealed by the New York Times.

-- / AFP - Getty Images

Tampa, Fla., socialite Jill Kelley, left, inadvertently triggered the FBI investigation of CIA Director David Petraeus by turning over anonymous threatening emails -- including one sent to Gen. John Allen -- to the FBI.

A senior defense official, also speaking on condition of anonymity, confirmed that Allen had received an anonymous email “some time ago” warning him to be careful around Kelley. The official, who had not seen the email but was generally familiar with its contents, said the general forwarded it to “proper authorities” within the military.

“He did the right thing,” the official said.

The defense official confirmed that the email also was forwarded to Kelley and her husband, Scott, but said it was not certain that Allen was the one who sent it to them. Allen did send Kelley an email referencing the anonymous note he had received, the official said.

The source close to Kelley and several law enforcement officials tell NBC News that Broadwell used multiple anonymous accounts to send the emails to Kelley and Allen. She “covered her tracks” by sending them from cybercafés, the source said.

Slideshow: Petraeus case: Cast of characters

ISAF via Reuters file

Meet the people who have been pulled into the scandal that caused Gen. David Petraeus to resign.

Launch slideshow

Meanwhile, defense officials tell NBC News that while there is no evidence that Allen and Jill Kelley engaged in an extramarital affair, there was enough “inappropriate” language in emails they exchanged to warrant an investigation by the Pentagon’s inspector general.

According to one official, who like the others spoke on condition of anonymity, a small number of emails contained language that could be considered “inappropriate” or even “suggestive.” 

But even without those, an investigation of the email correspondence between Allen and Kelley was inevitable given the circumstances, the officials said.

“We had no idea what was going on,” one said. “The last thing we want is to be accused of a cover-up,” regarding the Allen emails. 

Courtney Kube and Mike Brunker of NBC News contributed to this report.

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After investigating a potential case of "cyber-harassment" for several months, the FBI wrapped up its case after interviewing Paula Broadwell -- the biographer of former CIA director David Petraeus -- on Friday, Nov. 2, four days before the presidential election, a senior U.S. law enforcement official told NBC News.

It was the second time that FBI agents had questioned Broadwell in the probe and during both interviews she acknowledged having had an affair with Petraeus, the official said. Petraeus himself had been questioned a few days earlier and also acknowledged the affair, the first official said.

The dual interviews the week of Oct. 29 -- among the last to be conducted by the FBI in the case -- allowed the FBI to formally conclude there was no basis for criminal charges in the matter. This explains why the Director of National Intelligence James Clapper wasn't told about the probe until the following Tuesday, Nov. 6, election day, the official said.

The official offered new details about the FBI investigation -- and a more precise timeline of key events-- in order to rebut suggestions that senior law enforcement officials held back key information about the Petraeus matter until after the election.

The FBI and Justice Department's decisions on the case were not governed by the political calendar, the official asserted. Nor, the official said, were they influenced by a phone call from House Majority Leader Eric Cantor's office to the FBI on Oct. 31 asserting that it had heard from a FBI whistleblower who raised concerns that the Petraeus matter was being covered up or not being taken seriously.

Lawmakers question timing of Petraeus resignation

"I was contacted by an FBI employee concerned that sensitive, classified information may have been compromised and made certain (FBI Director Robert) Mueller was aware of these serious allegations and the potential risk to our national security,” Cantor said in a statement.

According to reporting by NBC’s chief justice correspondent Pete Williams, a senior law enforcement official said a call to a congressional staffer came from an agent who was initially involved in the investigation but who was later removed from the case because he knew an associate of one of the people being investigated.  The agent knew someone on the Hill and called that person, a Republican staffer, according to the official. But that phone call had no effect on either the course of the investigation, the involvement of Mueller -- who was following it closely long before Cantor called him -- or the decision to notify Clapper, the official says.

"This had nothing to do with the election," the official said. Moreover the official added, Cantor's office was told that the case was being actively investigated by the FBI when it raised the matter on Oct. 31, and so it would have been wrong for the FBI or Justice Department to inform higher level officials in the administration about the probe earlier -- because they were unsure at that point what they were dealing with. In the end, according to multiple officials, investigators determined there was no criminal wrongdoing.

According to the senior official, the investigation began several months ago when a woman reported to the FBI she had received anonymous-- and harassing -- emails from a person she didn't know. Multiple government officials tell NBC News that the woman was Jill Kelley, who lives in Tampa, Florida. Kelley and her husband, officials say, are close friends of the Petraeus family. Kelley was a volunteer social liaison to the MacDill Air Force Base in Tampa.

The FBI viewed the matter as a potential case of "cyber-harassment" and it was handled "regionally" with federal prosecutors working with the FBI on the matter, the official said. At first, neither Kelley nor the FBI knew who was sending the harassing emails-- because they came from accounts that were not immediately identifiable. But the FBI was eventually able to determine they came from Broadwell and then obtained access to her regular email account. It was only then that the FBI discovered, through her email exchanges with Petraeus, an apparent relationship between the two of them, the official said.

The FBI continued investigating the matter and was close to wrapping up the case late in October, the official said. Agents finally interviewed Petraeus the week of Oct. 29 and then re-interviewed Broadwell, allowing them to complete their investigation, according to multiple officials. It was only at that point that the decision was made to pass along information about the case to Clapper, the senior law enforcement official said, setting in motion the chain of events that led to Petraeus' resignation.

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NBC's Kristen Welker contributed to this report.