The Haaretz newspaper said at least 11 men are being held incommunicado in Jordan, including Khalid Shaikh Muhammad, the alleged mastermind of the September 11 attacks on the US, and Hanbali, accused of being al-Qaida's ally in South-east Asia.
"Their detention outside the US enables CIA interrogators to apply interrogation methods banned by US law and to do so in a country where cooperation with Americans is particularly close, thereby reducing the danger of leaks," Haaretz said.
But a Jordanian security official dismissed the story as "totally baseless".
The official, who declined to be named, said: "The allegations that surface every now and then that the US runs secret detention centres in the kingdom are totally baseless and seek to undermine the country's favourable human rights image abroad."
The paper attributed its information to international intelligence sources. A CIA official in Washington declined to comment.
International human rights groups have accused the US of circumventing guidelines on interrogation by shipping al-Qaida suspects to allied states where intense legal scrutiny is lacking.
Washington insists its interrogators operate within the law.
"US interrogators are known to threaten some detainees with shipping them off to Jordan if they don't cooperate"
author of Rumsfeld's War
US officials say incommunicado detentions in secret locations are essential for security and that many suspects held have provided valuable intelligence that have foiled planned attacks.
Jordan is seen as a key ally in the US-led "war on terror".
In Rumsfeld's War, a book drawing on declassified Pentagon documents, Washington Times correspondent Rowan Scarborough said Jordanian interrogators had helped US counterparts in handling al-Qaida suspects held at Guantanamo Bay, Cuba.
"US interrogators are known to threaten some detainees with shipping them off to Jordan if they don't cooperate," Scarborough said.
"Like other Middle Eastern countries, Jordan uses physical means to coerce confessions and vital intelligence information," he added.