Jan. 28, 2009 -- The CIA's station chief at its sensitive post in Algeria is under investigation by the U.S. Justice Department for allegedly raping at least two Muslim women who claim he laced their drinks with a knock-out drug, U.S. law enforcement sources tell ABC News.

The suspect in the case is identified as Andrew Warren in an affidavit for a search warrant filed in federal court in Washington, D.C. by an investigator for the State Department's Diplomatic Security Service.

Click here to read the affidavit.

Watch "World News with Charles Gibson" TONIGHT at 6:30 p.m. ET for the full report.

Officials say the 41-year old Warren, a convert to Islam, was ordered home by the U.S. Ambassador, David Pearce, in October after the women came forward with their rape allegations in September.

According to the affidavit, the two women "reported the allegations in this affidavit independently of each other."

The affidavit says the first victim says she was raped by Warren in Sept. 2007 after being invited to a party at Warren's residence by U.S. embassy employees.

She told a State Department investigator that after Warren prepared a mixed drink of cola and whiskey, she felt a "violent onset of nausea" and Warren said she should spend the night at his home.

When she woke up the next morning, according to the affidavit, "she was lying on a bed, completely nude, with no memory of how she had been undressed." She said she realized "she recently had engaged in sexual intercourse, though she had no memory of having intercourse."

According to the affidavit, a second alleged victim told a similar story, saying Warren met her at the U.S. embassy and invited her for a "tour of his home" where she said he prepared an apple martini for her "out of her sight."

The second victim said she suddenly felt faint and went to the bathroom where "V2 [victim 2] could see and hear, but she could not move," the affidavit says.

She told investigators Warren "was attempting to remove V2's her pants." The affidavit states, "Warren continued to undress V2, and told her she would feel better after a bath."

Alleged Rape Victims Tell Their Stories to Investigators

The alleged victim said she remembers being in Warren's bed and asking him to stop, but that "Warren made a statement to the effect of 'nobody stays in my expensive sheets with clothes on.'" She told investigators "as she slipped in and out of consciousness she had conscious images of Warren penetrating her vagina repeatedly with his penis."

The second victim told investigators she sent Warren a text message accusing him of abusing her and he replied, "I am sorry," the affidavit says.

According to the affidavit, when Warren was interviewed by Diplomatic Security investigators, he claimed he had "engaged in consensual sexual intercourse" and admitted there were photographs of the two women on his personal laptop. He would not consent to a search or seizure of the computer, leading investigators to seek the warrant.

According to the affidavit, a search of Warren's residence in Algiers turned up Valium and Xanax and a handbook on the investigation of sexual assaults.

The affidavit says toxicologists at the FBI laboratory say Xanax and Valium are among the drugs "commonly used to facilitate sexual assault."

"Drugs commonly referred to as date rape drugs are difficult to detect because the body rapidly metabolizes them," said former FBI agent Brad Garrett, an ABC News consultant. "Many times women are not aware they were even assaulted until the next day," he said.

The CIA refused to acknowledge the investigation or provide the name of the Algiers station chief, but the CIA Director of Public Affairs, Mark Mansfield, said, "I can assure you that the Agency would take seriously, and follow up on, any allegations of impropriety."

State Department Acting Spokesman Robert Wood issued a statement saying, "The U.S. takes very seriously any accusations of misconduct involving any U.S. personnel abroad. The individual is question has returned to Washington and the U.S. Government is looking into the matter."

U.S. officials were bracing for public reaction in the Muslim world, following the report of the allegation.

"It has the potential to be quite explosive if it's not handled well by the United States government," said Isobel Coleman, a senior fellow at the Council on Foreign Relations who specializes in women's issues in the Middle East.

"This isn't the type of thing that's going to be easily pushed under the carpet," she said.

U.S. Officials Say They Found Video Tapes

Both women have reportedly since given sworn statements to federal prosecutors sent from Washington to prepare a possible criminal case against the CIA officer.

Following the initial complaints, U.S. officials say they did obtain a warrant from a federal judge in Washington, D.C. in October to search the station chief's CIA-provided residence in Algiers and turned up the videos that appear to have been secretly recorded and show, they say, Warren engaged in sexual acts.

Officials say one of the alleged victims is seen on tape, in a "semi-conscious state."

The time-stamped date on other tapes led prosecutors to broaden the investigation to Egypt because the date matched a time when Warren was in Cairo, officials said.

As the station chief in Algiers, Warren played an important role in working with the Algerian intelligence services to combat an active al Qaeda wing responsible for a wave of bombings in Algeria.

In the most serious incident, 48 people were killed in a bombing in Aug. 2008 in Algiers, blamed on the al Qaeda group.

The Algerian ambassador to the United Nations, Mourad Benmehid, said his government had not been notified by the U.S. of the rape allegations or the criminal investigation.

Repeated messages left for the Warren with his parents and his sister were not returned.

No charges have been filed, but officials said a grand jury was likely to consider an indictment on sexual assault charges as early as next month.

"This will be seen as the typical ugly American," said former CIA officer Bob Baer, reacting to the ABC News report. "My question is how the CIA would not have picked up on this in their own regular reviews of CIA officers overseas," Baer said.

"From a national security standpoint," said Baer, 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," said Baer. "This is indicative of personnel problems of all sorts that run through the agency," he said.

"Rape is ugly in any context," said Coleman, who praised the bravery of the alleged Algerian victims in going to authorities. "Rape is viewed as very shameful to women, and I think this is an opportunity for the U.S. to show how seriously it takes the issue of rape," she said.

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