The announcement of John Durham's selection came as a report was published detailing the allegations of abuse by CIA agents.
Agents threatened to kill a key terror suspect's children and sexually assault another's mother, it is claimed.
The report was made in 2004 but only a heavily censored version appeared and a judge ordered fuller disclosure.
The justice department is reported to be reopening about a dozen prisoner abuse cases.
Also on Monday, President Barack Obama approved a new elite team to question terror suspects.
Republican anger
Mr Durham, who is already investigating the destruction of videotapes of CIA interrogations, was picked by US Attorney General Eric Holder.
Mr Holder said: "I fully realise that my decision to commence this preliminary review will be controversial
"In this case, given all of the information currently available, it is clear to me that this review is the only responsible course of action for me to take."
Special prosecutors in the US are independent figures appointed to investigate the possible wrongdoing of government officials or agencies.
Senior Republicans have already expressed anger at the decision.
Nine signatories of a letter to Mr Holder said they were "deeply disappointed" at a decision that "could have a chilling effect on the work of the intelligence community".
'Aggressive'
The declassified document released by the justice department said that one agent told key terror suspect Khalid Sheikh Mohammed that "we're going to kill your children" if there were further attacks on the US.
Another agent allegedly told Abd al-Rahim al-Nashiri, a suspect in the bombing of the USS Cole in 2000, that his mother would be sexually assaulted in front of him. The agent has denied the allegation.
In other incidents involving Mr Nashiri, he was allegedly threatened with an unloaded gun and had a power drill held near him which was repeatedly turned on and off.
Another incident involved an agent pinching an artery in a detainee's neck. As the man was passing out, the agent shook him awake, then repeated the action twice.
Ahead of the document's release, CIA Director Leon Panetta wrote on the agency's website that the report was "in many ways an old story" and that he would make "no judgments on the accuracy of the report or the various views expressed about it".
He said it was clear that the CIA had "obtained intelligence from high-value detainees when inside information on al-Qaeda was in short supply".
Mr Panetta said the CIA had been "aggressive" in seeking regular legal advice from the department of justice on its techniques.
He said his primary concern was "to stand up for those officers who did what their country asked and who followed the legal guidance they were given. That is the president's position, too."
But Mr Panetta also said: "This agency made no excuses for behaviour, however rare, that went beyond the formal guidelines on counter-terrorism."
Earlier on Monday, deputy White House press secretary Bill Burton confirmed there would be a new interrogation team for key terror suspects.
Correspondents say Mr Obama was concerned at the number of different agencies involved and he wanted to bring them together.
The new team will be called the High-Value Detainee Interrogation Group.
