Thierry Charlier / AFP - Getty Images file

US General John Allen looks on following a meeting of NATO Defense Ministers at NATO headquarters in Brussels in this Oct. 10, 2012, file photo.

Gen. John Allen, caught up and later cleared in a scandal over emails with a Florida socialite, is likely to withdraw from consideration for the job of top NATO commander, three U.S. military officials have told NBC News.

A Pentagon investigation last month cleared Allen of wrongdoing, but U.S. military officials said that Allen does not want to drag his family through a nomination process in which the emails would almost certainly come up.

Allen has spoken with Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff, and outgoing Defense Secretary Leon Panetta but he has not had the chance to meet with President Barack Obama to voice his concerns. A U.S. official said that Obama was aware of Allen’s feelings, and they would meet to discuss the nomination in the coming days.

“After 19 months in command in Afghanistan, and many before that spent away from home, Gen. Allen has been offered time to rest and reunite with his family before he turns his attention to his next assignment,” an official on Allen’s staff told NBC News.

Allen’s emails with the socialite, Jill Kelley, came to light during the investigation that ultimately brought down CIA director David Petraeus, who confessed to an extramarital affair with a separate woman.

Allen was previously the top American commander in Afghanistan. The White House had said after the Pentagon cleared him of wrongdoing that it would proceed with its nomination of Allen for supreme allied commander of NATO forces in Europe.

Kelley, who acted as a volunteer “social liaison” with military officials at MacDill Air Force Base, inadvertently triggered the investigation that led to Petraeus’ resignation by complaining to the FBI about anonymous emails she received.

FBI agents traced the allegedly threatening emails to Paula Broadwell, Petraeus’ biographer.

Just last weekend, Allen took part in a handover ceremony and passed command of the Afghan mission to Gen. Joseph Dunford. Allen delivered an emotional speech aimed mostly at the Afghan people and stressed their role in taking over security by mid-year. He said that Afghan forces were defending their own people and allowing the government to serve its citizens.

 “This is victory,” Allen said, according to Reuters. “This is what winning looks like.”

Last fall, defense officials told NBC News that while there was no evidence Allen and Kelley had had an affair, there was enough “inappropriate language” in them that they warranted an investigation by the Pentagon’s inspector general.

Obama nominated Allen last October for the NATO post but put a hold on the nomination while the Pentagon conducted its investigation.

In announcing the nomination, the president praised Allen’s stewardship of the Afghan mission and said that under his command “we have made important progress towards our core goal of defeating al-Qaida and ensuring they can never return to a sovereign Afghanistan.”

It remained possible that the president could ask Allen to reconsider and go ahead with the nomination, but a U.S. defense official does not think that will happen.

This story was originally published on Wed Feb 13, 2013 1:28 PM EST