Barack Obama has faith in General John Allen to continue commanding America's forces in Afghanistan while under investigation for alleged inappropriate communication with a woman at the centre of the scandal involving former CIA Director David Petraeus, the White House has said.
The Pentagon said on Tuesday that Allen was being investigated over alleged "inappropriate communications" with Jill Kelley, the woman who is said to have received threatening emails from the former lover of Petraeus, who resigned from his post on Friday.
"He [Obama] has faith in General Allen," White House spokesman Jay Carney told journalists, saying the US president believed Allen was doing a good job in Afghanistan.
Defence Secretary Leon Panetta said in a written statement that the FBI referred the matter to the Pentagon on Sunday and that he ordered a Pentagon investigation of Allen on Monday. Allen says he has done nothing wrong.
Allen succeeded Petraeus as the top US commander in Afghanistan in July 2011, and had been nominated to become the next commander of the US European Command and the head of NATO forces in Europe.
Panetta said that the Pentagon had begun an internal investigation into the emails from Allen, 58, to Kelley, 37.
"One of the prime goals of the Obama second term is to get the troops out of Afghanistan ... General Allen was giving Panetta a variety of options and scenarios for troop draw-downs," Al Jazeera's Rob Reynolds, reporting from Washington, said.
"That might all be out the window now and have to be redone."
A senior US official who has read the emails told the AP news agency that they were not sexually explicit or seductive.
"If people see these folks as being unfaithful in small things, how can you expect them to tell the truth about progress in Afghanistan? You cannot expect them to do that "
- Ray McGovern, retired CIA officer
The official said that those who have read the exchanges found them to be relatively innocuous even though they might be construed as unprofessional and flirty.
The official says the emails included pet names such as "sweetheart" and "dear" but did not offer evidence of an affair or classified information put at risk.
The official was not authorised to discuss the emails publicly and requested anonymity.
Meanwhile, the Reuters news agency reported that both Allen and Petraeus had recently intervened in a child custody battle on behalf of Kelley's twin sister, court documents show.
Petraeus and Allen wrote letters in September to the District of Columbia Superior Court in support of Natalie Khawam, as she sought to gain more visitation rights with her son, according to a review of the court file.
Meanwhile, FBI agents prepared a timeline of the Petraeus affair and searched the home of Paula Broadwell, the 40-year-old biographer with whom the 60-year-old had the extramarital relationship.
The resignation and his acknowledgement of an affair stunned Washington following the former general's highly disciplined and well-praised career.
Retired CIA officer Ray McGovern told Al Jazeera: "If people see these folks as being unfaithful in small things, how can you expect them to tell the truth about progress in Afghanistan? You cannot expect them to do that.
"What we have here is a situation where the troops know that they cannot trust their superiors."
It was Broadwell's threatening emails to Kelley, a Petraeus family friend, which led to the FBI's discovery of communications between Broadwell and Petraeus, indicating they were having an affair.
A Pentagon official said 20,000 to 30,000 pages of emails and other documents from Allen's communications with Kelley between 2010 and 2012 were under review.
He said he did not know whether Petraeus was mentioned in the emails.
Congress has said that legislators should have been told earlier about the affair.
The White House was not informed of the investigation until November 6, though agents began looking at Petraeus’ actions months earlier. Obama accepted Petraeus' resignation on November 9.
A federal law enforcement official, speaking on condition of anonymity, said the FBI had concluded relatively quickly that the email correspondence between Petraeus and Broadwell did not involve any security breach.
Without a security breach, it was appropriate not to notify Congress or the White House earlier, the official said.
FBI agents traced the alleged cyber harassment to Broadwell and discovered she was exchanging intimate messages with Petraeus.
The FBI's decision to refer the Allen matter to the Pentagon, rather than keep it itself, combined with Panetta's decision to allow Allen to continue as Afghanistan commander without a suspension, suggests that officials viewed whatever happened as a possible infraction of military rules rather than a violation of federal criminal law.
Allen was Deputy Commander of Central Command, based in Tampa, prior to taking over in Afghanistan. He also is a veteran of the Iraq war.