US officials have said the CIA's methods of interrogating suspected al-Qaeda leaders are too brutal, the New York Times reports.
FBI chief Mueller was reportedly advised against using CIA methods
Unnamed counter-terrorism officials told the paper that CIA methods were so severe, the FBI had directed its agents to stay out of many of the interviews.
The techniques are said to have been authorised by the Bush administration after the 9/11 attacks on the US.
None of the detainees, held in secret locations, are thought to be in Iraq.
The paper cites one case of a detainee who was subjected to a technique known as water boarding, in which a prisoner is strapped down, forcibly pushed under water and made to believe that he might drown.
Some have been hooded, soaked with water, roughed up and deprived of food, light and medication.
At least one CIA employee was disciplined for threatening a detainee with a gun during an interrogation.
The paper says FBI officials have advised their director, Robert Mueller, that the techniques would be prohibited in criminal cases.
Defenders of the secret interrogation rules say the methods stop short of torture and serious injury.
Current CIA officers are said to be worried that public outrage at the treatment of detainees in Iraq might lead to a closer examination of their treatment of al-Qaeda prisoners.
"Some people involved in this have been concerned for quite a while that eventually there would be a new president, or the mood in the country would change, and they would be held accountable," one was quoted as saying.
"Now that's happening faster than anybody expected."
The whereabouts of high-level al-Qaeda detainees is a closely guarded secret, and human rights groups have been denied access to the prisoners.
Officials say some have been sent abroad.
"There was a debate after 9/11 about how to make people disappear," a former intelligence official told the paper.
The government was advised that if the CIA was considering procedures which violated the Geneva Convention or US laws prohibiting torture and degrading treatment, it would not be held responsible if it could be argued that the detainees were in the custody of another country.