Even the head of the U.S. intelligence community now believes that its collection and storage of millions of call records was kept too secret for too long.

The American public and most members of Congress were kept in the dark for years about a secret U.S. program to collect and store such records of American citizens on a massive scale.The government’s legal interpretation of section 215 of the Patriot Act that granted the authority for this dragnet collection was itself a state secret.

Then came Edward Snowden, the former NSA contractor who leaked the court warrant authorizing the surveillance—along with troves of other top-secret documents. Since that first disclosure of the secret warrant, Director of National Intelligence James Clapper has had to defend the government’s activities against a skeptical Congress and wary public.

In an exclusive interview with The Daily Beast, Clapper said the problems facing the U.S. intelligence community over its collection of phone records could have been avoided. “I probably shouldn’t say this, but I will. Had we been transparent about this from the outset right after 9/11—which is the genesis of the 215 program—and said both to the American people and to their elected representatives, we need to cover this gap, we need to make sure this never happens to us again, so here is what we are going to set up, here is how it’s going to work, and why we have to do it, and here are the safeguards… We wouldn’t have had the problem we had,” Clapper said.

“What did us in here, what worked against us was this shocking revelation,” he said, referring to the first disclosures from Snowden. If the program had been publicly introduced in the wake of the 9/11 attacks, most Americans would probably have supported it. “I don’t think it would be of any greater concern to most Americans than fingerprints. Well people kind of accept that because they know about it. But had we been transparent about it and say here’s one more thing we have to do as citizens for the common good, just like we have to go to airports two hours early and take our shoes off, all the other things we do for the common good, this is one more thing.”

Since the first Snowden revelations in June, Clapper has declassified reams of material relating to the 215 program, including opinions and warrants signed by the top secret court that approves domestic snooping. But he has not publicly acknowledged until now his thoughts that the initial secrecy surrounding the program was ill-considered.

It’s a bit of an adjustment in Clapper’s public stance. The intelligence chief wrote in a letter to Sen. Ron Wyden, that the leak of the 215 program along with others “will do significant damage to the Intelligence Community’s ability to protect the nation.” (Of course, Snowden leaked more than the broad outlines of the program that Clapper said he would’ve liked disclosed.)

Ben Wizner—a legal adviser to Snowden and the director of the American Civil Liberties Union’s Speech, Privacy and Technology Project—said he agreed with Clapper’s current assessment. “If Clapper is suggesting that the American people should have been consulted before the NSA engaged in a mass phone call tracking program, I emphatically agree,” he said “Whether we would have consented to that at the time will never be known, we are now having a debate in Congress and in the courts that we should have had then.”

Last month, President Obama defended the 215 program in a major speech on government surveillance programs. But he also ordered a government review into the feasibility of a third party storing the call records as opposed to the government.

While this option is studied, Obama placed new limits on when intelligence analysts can query the database of call records for this interim period. These new limits mean that phone calls will only be pursued that are two steps, as opposed to three steps, away from a phone number suspected to be linked to a terrorist group. Also an analyst will only be allowed to query the call records after a “judicial finding or in the case of a true emergency,” Obama said.

Clapper still defends the 215 program, too. The storage of the phone records allows NSA analysts to connect phone numbers of suspected terrorists overseas to a possible network inside the United States. Other U.S. intelligence officials say its real value is that it saves work for the FBI and the NSA in tracking down potential leads by ruling out suspicious numbers quickly.

In the interview Clapper said the 215 program was not a violation the rights of Americans. “For me it was not some massive assault on civil liberties and privacy because of what we actually do and the safeguards that are put on this,” he said. “To guard against perhaps these days low probability but a very (high) impact thing if it happens.” Clapper compared the 215 program to fire insurance. “I buy fire insurance ever since I retired, the wife and I bought a house out here and we buy fire insurance every year. Never had a fire. But I am not gonna quit buying my fire insurance, same kind of thing.”

Snowden’s disclosure of the 215 program for Clapper also had personal consequences. Less than a week after the Guardian and Washington Post published their stories based on the secret court order to Verizon, opinion writers and members of Congress dug up Clapper’s own testimony from March 12, 2013 before the Senate Select Committee on Intelligence.

In that testimony, Clapper was asked directly by Sen. Ron Wyden, a Democrat from Oregon: “Does the NSA collect any type of data at all on millions or hundreds of millions of Americans?” At the time Clapper responded, “No sir.” Wyden then asked, “they do not?” Clapper responded, “Not wittingly. There are cases where they could inadvertently, perhaps collect, but not wittingly.”

At the time, the 215 program was still highly classified. Clapper later told Andrea Mitchell of NBC News that he believed the question was a bit like when he had stopped beating his wife and therefore was difficult to answer with a yes or no. “So I responded in what I thought was the most truthful or least untruthful manner, by saying, ‘No,’” he told Mitchell.

Many members of Congress have called for Clapper to resign because of this exchange and his subsequent explanation, alleging that Clapper lied to Congress and committed perjury.

In the interview with Mitchell, Clapper said he believed that “collection of a U.S. person’s data would mean taking the books off the shelf, opening it up and reading it.” The 215 program, in contrast, is the mass collection of nearly every phone call record made through a U.S. telecommunications company, but not the contents of those calls themselves. Sometimes known as telephony metadata, this information is comprised of the time, duration and number dialed of a phone number. Millions and millions of people are impacted by it.

At the time, Joel Brenner, a former inspector general for the NSA, defended Clapper saying Wyden was wrong to ask him a question for which he knew the answer was classified.

But Clapper told The Daily Beast that he simply misunderstood Wyden’s question. At the time of the hearing last March, Congress had just finished consideration of a bill to renew the Foreign Intelligence Surveillance Act (FISA). Section 702 of that legislation gives the National Security Agency the authority to collect the electronic communications of non-U.S. persons. In his question, Wyden asked initially if the United States had collected “dossiers” on American citizens and referred to an answer to this question by then NSA director, Keith Alexander.

“I was not even thinking of what he was asking about, which is of course we now all know as section 215 of the Patriot Act governing the acquisition and storage of telephony business records metadata,” Clapper said. “Wasn’t even thinking of that.” The director of national intelligence said he thought Wyden’s question was actually about section 702 of FISA.

“The allegation about my lying and committing perjury I think are disproven by my labored amplification when I said, ‘if there is, it’s inadvertent collection,’ meaning when we’re collecting overseas under section 702, and if we inadvertently collect which we may not know at the time, U.S. persons data, that’s what I meant by inadvertent. That comment would make absolutely no sense whatsoever in the context of section 215.”

At the time of the Mitchell interview, the U.S. government was still in the process of declassifying elements of the FISA 702 program. “There is only one person on the planet who actually knows what I was thinking,” Clapper said of his testimony from last March. “Not the media, and not certain members of Congress, only I know what I was thinking.”