The career of the top US commander in Afghanistan is now in jeopardy because of the investigation into the sex scandal involving David Petraeus, the former top commander in Iraq and Afghanistan who resigned as CIA director last week.
The Pentagon said on Tuesday that General John Allen is under investigation for alleged "inappropriate communications" with Jill Kelley, the woman who is said to have received threatening emails from Petraeus' former lover.
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 succeeded Petraeus as the top American commander in Afghanistan in July 2011 and had been nominated to become the next commander of the US European Command and the commander of NATO forces in Europe.
But according to a White House statement, President Barack Obama has held Allen’s nomination at Panetta’s request.
Panetta said that the Pentagon had begun an internal investigation into thousands of pages of emails from General John Allen to a second woman involved in the Petraeus case.
“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. That might all be out the window now and have to be redone,” Al Jazeera's correspondent Rob Reynolds in Washington said.
Breach of trust
"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
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 Petraeus had an affair that led to his abrupt resignation on Friday.
The resignation and his acknowledgement of an affair stunned Washington because of 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 a Petraeus family friend, 37-year-old Jill Kelley, 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 are under review.
He would not say whether they involved sexual matters or whether they are thought to include unauthorised disclosures of classified information.
He said he did not know whether Petraeus is mentioned in the emails.
Allen has denied any wrongdoing.
Congress left out
Meanwhile, Congress has been in an uproar with legislators saying they 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.
Absent 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 a private Gmail account.
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, suggested strongly 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.