"I hope that the judicial process can be put in place which means that Guantanamo Bay can close," he said during his weekly question session in the House of Commons.
"However, the reason I always qualify my answer on this is as follows: this arose out of the worst terrorist act this world has ever known in which 3,000 totally innocent people lost their lives in New York," he said. "And those people who were picked up in Afghanistan (and sent to Guantanamo) were people who were engaged in helping those reactionary forces there to defeat American and British troops."
Nearly 500 people are being held in Guantanamo, some for several years, but only a handful have been charged.
Blair repeated the assertion he has made previously that the camp is an anomaly.
"That's why it has to end; but I'm afraid I will always when I answer questions on this draw attention to the circumstances in which it was introduced," he said.
Menzies Campbell, the Liberal Democrats' acting leader, had asked Blair about Guantanamo and about what some see as an unfair disparity in the extradition rules between Britain and the U.S.
The prime minister responded with an angry attack on the party's criticisms of the United States.
"I just sometimes wish they would spend just a little bit of the amount of the effort they do attacking the United States on understanding why these issues of international terrorism are so important, why it is important that we actually stand with our allies" in fighting terror, he said.
Critics say it is unfair that the United States and Britain impose different legal requirements for extradition, as the U.S. Senate has not ratified a U.S.-British extradition treaty that Blair's government already has brought into force.
Blair said Britain wanted America to put the new rules in place, but added that "we still believe it is right that we have these extradition provisions in place."