New Yorker writer Seymour Hersh, discussing the book set for release Monday, said senior military and national security officials received warnings from subordinates in 2002 and 2003 about such mistreatment.
Hersh said Rice held meetings on the issue and it was brought to the attention of Defense Secretary Donald H. Rumsfeld before it "disappeared."
Rice said that in the fall of 2002, the White House "was made aware that there were some concerns that people might have been held at Guantanamo who didn't meet the definition of unlawful combatant.
"There were also early on ... some concerns about conditions of overcrowding. But nothing that suggested, to my recollection, that there were abuses ... going on at Guantanamo, and certainly nothing that would suggest the kind of thing that went on in Abu Ghraib," she said, referring to the infamous Iraqi prison.
Nearly all the approximately 585 detainees at the base were captured in Afghanistan after U.S. forces invaded in October 2001 in response to the Sept. 11 attacks.
The U.S. government defines an enemy combatant as "an individual who was part of or supporting Taliban or al Qaeda forces, or associated forces that are engaged in hostilities against the United States or its coalition partners."
A person classified as an enemy combatant can be held without being charged with a crime and without legal representation until the conflict has ended.
Rice said in a broadcast interview that when the administration learned there might be people at Guantanamo who failed to meet the standard of unlawful combatant, "We looked at the cases, put together a process to try and make sure that the right people were being held."
She also said the United States worked hard to improve conditions at the Cuban prison. "I do not recall being told of anything concerning prisoner abuse," Rice said.
Rice said she and a deputy, John Gordon, talked about conditions at Guantanamo and worked with the Pentagon to ease overcrowding. "I was also informed that there were concerns that people might have been held there who shouldn't have been held there. We held several meetings then, and all of this was referred to the Defense Department for action," she said.
Even before release of "Chain of Command: The Road From 9/11 to Abu Ghraib," the Pentagon had issued a public statement about inquiries into the book by Hersh, who is widely credited with disclosing the Abu Ghraib prison scandal.
"It appears that Mr. Seymour Hersh's upcoming book apparently contains many of the numerous unsubstantiated allegations and inaccuracies which he has made in the past based upon unnamed sources," the Pentagon said in a statement Friday.
The statement said detainee operations in Afghanistan, Iraq and elsewhere "have been examined extensively" by the Defense Department and an independent panel, and that investigations continue.
"Thus far, these investigations have determined that no responsible official of the Department of Defense approved any program that could conceivably have authorized or condoned the abuses seen at Abu Ghraib," the statement said.
The Pentagon urged that if any of Hersh's anonymous sources want to come forward and offer evidence "to the contrary, the department welcomes them to do so."
Hersh, who appeared on a Sunday morning talk show, said that after his New Yorker series on Abu Ghraib, "people who worked inside the White House came to me and said, 'Look, this is much more far-reaching than you think.'"