John Bellinger, a legal advisor to U.S. Secretary of State Condoleezza Rice, dismissed the claims as "absurd."
Bellinger, speaking in Brussels, said the allegations "undermine the cooperation between the U.S. and Europe."
A preliminary European Parliament report last week said that the United States had made more than 1,000 undeclared flights over European territory since 2001.
It also stated that the CIA had "on several occasions" kidnapped and illegally detained terror suspects on EU territory and flown them to countries that use torture, a practice known as extraordinary rendition.
(AFP)