John Bellinger says he was not suggesting the old rules "be discarded" or "not be followed" when he questioned their sacredness in an interview with The Financial Times this week.
Bellinger, legal adviser to Secretary of State Condoleezza Rice, said the Bush administration had set out on a "new course" in its treatment of terrorist suspects.
And he questioned whether the Geneva Conventions should be "the immutable legal holy grail as to what the rules ought to be in the 21st century."
His comments brought a rebuke from the European Union's counterterrorism coordinator, Gijs de Vries, who told Saturday's New York Times "respecting the rules, not bending them," was "essential to our credibility and hence to our effectiveness in the fight against terrorism."
De Vries cautioned Western governments not to sacrifice their principles in the fight against terrorism.