"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.
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.