In a statement made before leaving for a trip to Europe, Ms Rice stopped short of confirming the existence of reported detention centres, but defended the practice of “rendition”, or flying suspected terrorists to third countries for interrogation.
"Renditions take terrorists out of action and save lives," she said, insisting that they were permissible under international law when traditional extradition was not a workable option.
"It is up to those governments and their citizens to decide if they wish to work with us to prevent terrorist attacks against their own country or other countries, and decide how much sensitive information they can make public," she said.
Ms Rice argued the interrogations were conducted according to US and international law and had produced intelligence that thwarted attacks and saved lives, including in Europe.
"The United States has fully respected the sovereignty of other countries that have cooperated in these matters," Ms Rice said, implying that any European nations that may have provided secret prisons did so willingly.
Torture denied
But Secretary Rice denied the use of torture, saying the US respected the Convention Against Torture and did not “permit, tolerate or condone torture under any circumstances."
"The United States does not transport, and has not transported, detainees from one country to another for the purpose of interrogation using torture,” her statement said.
She said authorities were dealing with often stateless "enemy combatants" who fit into no traditional military or criminal justice system.
She said international law allowed for the detention of enemy combatants for "the duration of hostilities".
"The US does not seek to hold anyone for a period beyond what is necessary to evaluate intelligence or other evidence against them, prevent further acts of terrorism, or hold them for legal proceedings."
European tour
Ms Rice made the comments before flying to Germany on a trip that will also take her to Romania, Ukraine and Brussels for a NATO ministerial meeting.
European governments have expressed outrage over reports of a network of secret Soviet-era prisons in Eastern Europe and that flights carrying al-Qaeda prisoners went through European airports.
Last week Britain, as current European Union president, sent a letter to Washington seeking clarification over the reports.
There was no immediate EU response to the latest US statement, but British Foreign Secretary Jack Straw welcomed Ms Rice's remarks.
"All European countries fully share the determination expressed here by the US to protect our citizens from the threat of terrorism, clearly while operating within international law and our treaty obligations," he said.
In Berlin, a government spokesman said officials had a list of more than 400 overflights and landings by planes suspected of being used by the CIA that it plans to ask Ms Rice about during her visit.
Several countries have denied they provided prison sites.
Romania was one country named by rights groups for allegedly hosting secret CIA prisons.
The prison controversy may threaten an accord allowing US military bases in Romania due to be signed during Ms Rice’s visit to Bucharest on Tuesday.