Rice, leaving on a European tour, made no mention of the reported prisons but defended moving terror suspects around for interrogation, and denied using torture "under any circumstances".
"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," Rice said in a statement read at Andrews Air Force base outside Washington.
"So now, before the next attack, we should all consider the hard choices that democratic governments must face. We can all best meet this danger if we work together."
Recent press reports have said that the CIA maintains a network of secret detention facilities in Eastern Europe, Afghanistan, Thailand and elsewhere, where it holds terrorist suspects to circumvent US laws protecting detainees, particularly restrictions on the use of torture.
Aircraft, allegedly operated by the CIA, have been spotted at airports in Finland, Germany, Hungary, Iceland, Italy, Poland, Portugal, Spain and Sweden as well as Morocco.
"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"
US secretary of state
Rice's widely expected statement came as she left on a four-nation tour through Europe on Monday, likely to be dominated by reports of "black site" interrogation centres and clandestine CIA flights for Islamic militants.
The European Union is investigating the reports. Last week it sent Washington a request for clarification of the reported practices that some media suggested might violate international laws.
The Netherlands warned Washington last week that if it continued to be secretive about reports of prisons in eastern Europe, Dutch contributions to US-led military missions could be affected.
Ben Bot, the Dutch foreign minister, told parliament: "The US should stop hiding. It will all come out sooner or later."
But Rice said the US administration complied with its constitution, its laws and treaty obligations. "The United States has respected, and will continue to respect, the sovereignty of other countries," she said.
She was unapologetic about the use of tough tactics to combat terrorism since the 11 September 2001 attacks, particularly the practice of "rendition," or transporting suspects to another country for interrogation.
"Renditions take terrorists out of action and save lives," she said.
She cited France's use of rendition to transfer the terrorist "Carlos the Jackal" from Sudan where he was captured in 1994, which she said was ruled legal by the European human rights commission.
Invoking the argument that the primary duty of governments is to protect their citizens, Rice said they were dealing with essentially stateless terror suspects who fit into no traditional military or crimial justice system.
The Netherlands FM Ben Bot: It
will all come out sooner or later
"We have had to adapt. Other governments are now also facing this challenge," she said. Suspects had to be interrogated to obtain "potentially significant, life-saving intelligence".
Rice said that the United States respected the letter of the Convention Against Torture and "does not permit, tolerate or condone torture under any circumstances".
She said that the US had not transported and would not transport detainees from one country to another to be questioned using torture.