The CIA has removed its station chief in Algeria amid a US Justice Department investigation into allegations he raped at least two women, US media reports say.

Andrew Warren, an American convert to Islam, was ordered home in October after two women came forward last September with rape allegations in separate incidents, ABC News reported.

Warren had been in his post since September 2007.

Both women had provided sworn statements to federal prosecutors in preparation for a possible criminal case against Warren, ABC News said, with a grand jury likely to consider an indictment on sexual assault charges as early as next month.

The allegations could potentially deal a major blow to the US image abroad at a time when new President Barack Obama has called for "a new way forward, based on mutual interest and mutual respect" with the Muslim world.

Algeria in particular is seen as a hotspot because of the presence of al-Qaeda's North African branch there. A suicide bombing in August in Issers, 60km east of Algiers, left 48 people dead.

Warren's case "will be seen as the typical ugly American," former CIA officer Bob Baer told ABC News.

"My question is how the CIA would not have picked up on this in their own regular reviews of CIA officers overseas."

"From a national security standpoint," the alleged rapes would be "not only wrong but could open him up to potential blackmail and that's something the CIA should have picked up on," he added.

"This is indicative of personnel problems of all sorts that run through the agency."

According to the affidavit, a copy of which was provided by the television network, the first alleged victim said she was raped by Warren, 41, in September 2007 after being invited to a party at Warren's residence with US embassy employees where she was served a mixed drink of cola and whiskey.

Later in the evening, she felt ill and woke up the next morning nude after being apparently raped. She said she had no recollection of having intercourse.

The second alleged victim described a similar incident that occurred in February 2008.

CNN said pills and other evidence, including about a dozen videotapes showing the officer engaged in sexual acts, turned up when a search warrant was executed on the officer's residence.

The affidavit said Valium and Xanax, drugs FBI toxicologists described as "commonly used to facilitate sexual assault," were found in Warren's home in Algiers.

When interviewed by diplomatic security investigators, Warren claimed he had "engaged in consensual sexual intercourse," according to the affidavit.