The widening probe into Petraeus's extramarital affair has raised questions about the US commander in Afghanistan, distracting from talks over a looming budget crisis and efforts to fill high-level positions in Obama's second term.
The White House on Tuesday expressed confidence in John Allen after the four-star general was linked to the scandal, which saw Petraeus resign in disgrace after a sterling career just three days after Obama's re-election.
Allen was placed under investigation after FBI agents probing email threats sent by Petraeus' mistress stumbled upon a vast trove of messages Allen sent to another married woman at the heart of the scandal.
According to a senior Pentagon official, the married general denies any sexual liaison with 37-year-old Tampa socialite Jill Kelley, but the "sheer volume" of correspondence could amount to "conduct unbecoming an officer."
Due to face lawmakers this week for a hearing to confirm his promotion to the post of NATO's supreme commander in Europe, Allen will now return to Kabul and remain in charge of allied forces in Afghanistan until the probe is over.
"The president thinks very highly of General Allen and of his service to his country, as well as the job he has done in Afghanistan," White House spokesman Jay Carney told reporters.
"He has faith in General Allen," Carney said, adding that the White House had known about the Allen strand to the investigation since Friday.
Defense Secretary Leon Panetta, currently on an official visit to Australia, on Wednesday urged against jumping to any conclusions about Allen and said the general has his "continued confidence."
Petraeus resigned last week when it became clear that his affair with 40-year-old military reservist Paula Broadwell, who wrote a fawning biography of him, would become public.
FBI agents stumbled on the liaison after a complaint from Kelley -- a close friend of both Petraeus and Allen -- who told a federal agent that she had received threatening emails, which investigators later traced to Broadwell.
The threatening emails she had sent to Kelley -- who told investigators she did not know Broadwell -- suggest the biographer was jealous of the socialite's rapport with the generals at US Central Command in Florida.
The Wall Street Journal cited an official as saying Broadwell had sent a series of critical emails about Kelley to senior generals under the pseudonym KelleyPatrol, including one to Allen in which she called Kelley a "seductress."
The Pentagon is meanwhile investigating Allen after FBI agents found 20,000 to 30,000 pages of his correspondence, including hundreds of emails to Kelley.
A Pentagon official said some of the emails were seen as "flirtatious" but that only an investigation could determine if Allen, who is married, had broken the law or violated military regulations.
Petraeus and Broadwell were interviewed by investigators and both admitted to the affair, which the retired four-star general told friends he ended about four months ago.
Petraeus had been due to testify to Congress this week on the September 11 assault in Benghazi, Libya that killed four Americans, including US ambassador Chris Stevens and two former Navy SEALs working for the CIA.
Democratic Senator Dianne Feinstein told CNN she expected Petraeus would still agree to testify at a later date, adding that she had seen nothing to link the sex scandal to Benghazi.
Petraeus took command of the CIA 14 months ago, retiring from the military after a storied career in which he commanded troops in Iraq and Afghanistan.
The general, who presided over the 2007 troop "surge" in Iraq, is widely credited with turning the tide of the US war there, though his efforts have been less successful in Afghanistan.
Broadwell has hired renowned Washington power attorney Robert Muse to represent her. No criminal charges have been filed, but FBI agents searched her North Carolina home earlier this week and seized several boxes and pictures.
The Federal Bureau of Investigation has also come under scrutiny.
The Wall Street Journal reported that the FBI agent Kelley contacted about the threatening emails, a personal acquaintance of hers, brought the matter to the attention of Republican lawmakers.
The agent apparently believed the bureau was not moving aggressively enough with the investigation, suspecting that his superiors were keen to protect the Democratic president from the fallout.
FBI supervisors had earlier thrown the agent off the case after he became "obsessed" with the matter, the Journal said.
It quoted one official as saying the agent had sent shirtless photos to Kelley and was currently under internal investigation.