There was no immediate comment from Clapper's office Thursday on his testimony in March.
The public is now on notice that the government has been collecting data-- even if not listening to the conversations -- on every phone call every American makes, a program that has operated in the shadows for years, under President George W. Bush, and continued by President Barack Obama.
"It is very likely that business records orders like this exist for every major American telecommunication company, meaning that if you make calls in the United States the NSA has those records," wrote Cindy Cohn, general counsel of the nonprofit digital rights group Electronic Frontier Foundation, and staff attorney Mark Rumold, in a blog post.
Without confirming the authenticity of the court order, White House spokesman Josh Earnest said such surveillance powers are "a critical tool in protecting the nation from terror threats," by helping officials determine if people in the U.S. who may have been engaged in terrorist activities have been in touch with other known or suspected terrorists.
House Intelligence Committee Chairman Mike Rogers, R-Mich., stressed that phone records are collected under court orders that are approved by the Senate and House Intelligence committees and regularly reviewed.
And Senate Democratic leader Harry Reid of Nevada played down the significance of the revelation.
"Everyone should just calm down and understand that this isn't anything that's brand new," he said. "This is a program that's been in effect for seven years, as I recall. It's a program that has worked to prevent not all terrorism but certainly the vast, vast majority. Now is the program perfect? Of course not."
But privacy advocates said the scope of the program was indefensible.
"This confirms our worst fears," said Alexander Abdo, a staff attorney with the American Civil Liberties Union's National Security Project. "If the government can track who we call," he said, "the right to privacy has not just been compromised - it has been defeated."
Rep. Jim Sensenbrenner, R-Wis., who sponsored the USA Patriot Act that governs the collection, said he was "extremely troubled by the FBI's interpretation of this legislation."
Attorney General Eric Holder sidestepped questions about the issue during an appearance before a Senate subcommittee, offering instead to discuss it at a classified session that several senators said they would arrange.
House Speaker John Boehner called on Obama to explain why the program is necessary.
It would "be helpful if they'd come forward with the details here," he said.
The disclosure comes at a particularly inopportune time for the Obama administration. The president already faces questions over the Internal Revenue Service's improper targeting of conservative groups, the seizure of journalists' phone records in an investigation into who leaked information to the media, and the administration's handling of the terrorist attack in Libya that left four Americans dead.
At a minimum, it's all a distraction as the president tries to tackle big issues like immigration reform and taxes. And it could serve to erode trust in Obama as he tries to advance his second-term agenda and cement his presidential legacy.
The Verizon order, granted by the secret Foreign Intelligence Surveillance Court on April 25 and good until July 19, requires information on the phone numbers of both parties on a call, as well as call time and duration, and unique identifiers, according to The Guardian.
It does not authorize snooping into the content of phone calls. But with millions of phone records in hand, the NSA's computers can analyze them for patterns, spot unusual behavior and identify "communities of interest" - networks of people in contact with targets or suspicious phone numbers overseas.
Once the government has zeroed in on numbers that it believes are tied to terrorism or foreign governments, it can go back to the court with a wiretap request. That allows the government to monitor the calls in real time, record them and store them indefinitely.
Poll: Which new movie do you most want to see this holiday weekend?