But the latest controversy has already spawned a major lawsuit against Verizon, one of the telephone companies involved, and members of Congress expressed unease over what they see as gradual erosion of privacy rights.
The lawsuit, filed in New York on Friday, seeks five billion dollars from Verizon in damages, alleging the company has broken the law by agreeing to provide the National Security Agency with telephone records of its clients.
The plaintiffs argue phone companies should not cooperate with the NSA that specialises in electronic espionage without a proper court warrant based on well-grounded "suspicion of terrorist activity or other criminal activity".
But in his weekly radio address, Mr Bush assurred the public the secret program did not target innocent private citizens.
"It is important for Americans to understand that our activities strictly target Al-Qaeda and its known affiliates," he said.
But he gave no answer to questions raised on Capitol Hill as to why a programm with a purported narrow target would need such a massive database.
The existence of the program was first disclosed Thursday by the USA Today newspaper, which said the database compiled by the NSA following the September 11, 2001 attacks contained phone records of tens of millions of Americans provided by AT&T, Verizon and BellSouth.
Mr Bush said the intelligence activities he had authorised were "lawful" and members of Congress from both sides had been adequately briefed.
"The privacy of all Americans is fiercely protected in all our activities," he insisted. "The government does not listen to domestic phone calls without court approval."
The latest controversy follows accusations that the president may have broken the law when he authorised the NSA to conduct wiretaps of international phone calls made by Americans suspected of terrorist ties without a requisite court warrant.