Citing current and former government officials, The New York Times on Sunday said President George Bush signed a still-classified directive that gave the CIA a broad power to operate without case-by-case approval from the White House in transfer of suspects - a process known as rendition.
The rendition programme has been under scrutiny in recent weeks after several former detainees complained of inhuman treatment.
Since the September 11 attacks on the United States, the CIA has flown 100 to 150 suspects to countries including Egypt, Syria, Saudi Arabia, Jordan and Pakistan, former officials told the newspaper.
One current senior US official said the programme had been aimed only at those suspected of knowledge about terrorism operations and were transferred with promises they would not be tortured.
He did not dispute there had been mistreatment on some occasions, but said no one had died.
A half a dozen current and former officials said the Bush administration might have turned a blind eye to torture.
"I really wonder what they are doing, and I am no longer sure what I believe," one former senior official was quoted as saying.
The Bush administration has publicly said the United States did not hand over people to be tortured.