Reports say the officer was recalled to the US after the accusations
The CIA's station chief in Algeria is under investigation after two separate allegations of rape, US media report.
Two Algerian women came forward last September saying they had been sexually assaulted by the man while at his home in Algiers, ABC News says.
The man, identified in court documents as Andrew Warren, was recalled in October while the US Justice Department investigated, officials said.
Mr Warren, 41, had been stationed in Algiers since 2007.
Both alleged victims have provided sworn statements to prosecutors ahead of a possible criminal case, ABC News reported.
One of the women said she had been drinking at a party at the officer's house in September 2007 when she became suddenly ill and passed out.
She woke up later thinking she had had intercourse, but unable to remember for sure, court documents say.
The second woman approached embassy staff claiming the man had sexually assaulted her at his home last February.
Court documents said investigators found drugs associated with date-rape in the officer's Algiers home, ABC News reported.
A state department spokesman said: "The United States takes very seriously any accusations of misconduct involving any US personnel abroad."
A CIA station chief runs the agency's operations in foreign countries while managing relationships with the host nation's security services.