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Rubio directly said Cruz was wrong to vote to curb the NSA's authority to collect such data earlier this year, in the wake of the terror attacks in San Bernardino, California.
"We are now at a time when we need more tools, not less tools, and that tool we lost - the metadata program - was a valuable tool that we no longer have at our disposal," Rubio said.
Cruz countered by saying Rubio was spreading "knowingly false" information about his record and the bill he voted for, the USA Freedom Act. He cited conservative radio host Mark Levin to claim Rubio's attacks against him were false and "Alinsky-like," a reference to Saul Alinsky, a community organizer with ties to President Barack Obama.
"Marco knows what he is saying isn't true," Cruz said. "What he knows is that the old program covered 20% to 30% of phone numbers to search for terrorists. The new program covers nearly 100%. That gives us greater ability to stop acts of terrorism and he knows that's the case."
But Rubio held his ground.
"Let me be very careful in answering because I don't think national television in front of 15 million people is the place to discuss classified information," he said.
"So let me just be very clear: There's nothing that we are allowed to do under this bill that we could not do before," he continued. "This bill did, however, take away a valuable tool that allowed the National Security Agency and other intelligence agencies to quickly and rapidly access phone records and match them up with other phone records to see who terrorists have been calling."
Rubio added: "Because I promise you, the next there's an attack on the country, the first thing people are going to want to know is why we didn't know about it and why didn't we stop it. And the access better not be because we didn't have access to records."
Paul then backed up Cruz, arguing that the USA Freedom Act didn't undermine national security in any way. He also dinged Rubio over his support in drafting a 2013 comprehensive immigration-reform bill along with Sen. Chuck Schumer (D-New York), among others.
"Marco has more of an allegiance to Chuck Schumer and the liberals than he does to conservative policy," Paul said.
New Jersey Gov. Chris Christie (R), meanwhile, got in on the exchange with an at-large quip at the senators.
"If your eyes are glazed over like mine, this is what it's like to be on the floor of the US Senate," he said. Senators, he said, argue about "how many angels are on the head of a pin."