White House Unsure What Files Edward Snowden Has

June 27, 2013 — -- The Obama administration expressed heightened alarm today over fugitive leaker Edward Snowden's stash of secret spy files, as a new batch of highly classified papers spilled across the Internet, revealing how the U.S. government collected online data in bulk.

A top aide to President Obama conceded that the administration doesn't know yet all of what Snowden allegedly swiped while he was a National Security Agency contractor before he slipped to Hong Kong earlier this month and then to Moscow.

"Look, I don't know with certainty what Mr. Snowden has," Deputy National Security Advisor Ben Rhodes told reporters in Dakar, Senegal. "That's something that we're actively seeking to determine."

Snowden has already compromised "very classified programs" by leaking them to three newspapers and by taking files overseas, Rhodes said, acknowledging that the government still believes he's carrying the files on his person.

"So we have very strict protocols for how to handle classified information. It doesn't involve getting on a plane and going to Hong Kong and then getting on a plane and going to Russia," Rhodes said.

The intelligence community is conducting both a damage assessment related to the leaks so far and a forensic audit of computers and systems that Snowden had access to, sources told ABC News. But the sources fear Snowden may have hidden his tracks well enough at NSA to make it impossible to determine everything he copied.

Snowden, who worked as an undercover computer specialist with the CIA before contracting with the NSA, is said to be in hiding in the "transit area" of a Moscow airport. Top U.S. officials have urged Russia to expel Snowden, who has been charged with espionage in the U.S., but Russia's President Vladimir Putin said earlier this week that Snowden is a "free person."

TIMELINE: Edward Snowden's Life as We Know It

During his goodwill trip to Africa, President Obama said today that he had not personally appealed to Putin to send Snowden back to the U.S. to face justice, nor was he prepared to pull out all the stops to collar him.

"No, I am not going to be scrambling jets to get a 29-year-old hacker," Obama told reporters on Thursday morning, apparently referring to the chance Snowden could take a flight from Moscow to Havana, Cuba, which would travel over American airspace.

Did Obama Speak Too Soon on NSA File Harm?

While he is still concerned that Snowden could release more classified documents, Obama said he believed the real damage had already been done.

"I get why this is a fascinating issue," Obama said. "But in terms of U.S. interests, the damage was done with the first leaks."

But soon after the President spoke, The Guardian newspaper posted more U.S. intelligence files classified at the "SECRET" level and higher, as well as "NOFORN," meaning it was too sensitive to be distributed to foreign allies.

The NSA and Department of Justice documents detailed a decade of collection of email data mostly of foreigners but also U.S. persons, which top prosecutors determined was not constitutionally protected because it was strictly time, date, Internet Protocol addresses – unique to each individual computer -- and email addresses. The actual content of the messages was not collected by NSA under the program codenamed "Stellar Wind," according to The Guardian.

To collect the content of emails, a warrant was required from the most secret bench in the U.S., the Foreign Intelligence Surveillance Court, which convenes in Washington behind closed doors in an eavesdrop-proof chamber. The FISA court every 90 days renewed authority to collect the bulk email metadata – which was gathered primarily for use in counterterrorism – between late 2001 and 2011, when the program was shut down, the Guardian reported.

Most of the communications collected by the NSA were among people outside the U.S. but eventually messages originating inside the U.S. also were gathered, as detailed by the U.K.-based newspaper.

"The revelations about our government's spying raise new and troubling questions about the extent to which the government is monitoring Americans' private lives, including whom we email or chat with and what websites we visit," said Alex Abdo, staff attorney with the American Civil Liberties Union's National Security Project.

The program was terminated in 2011, not because of privacy concerns, but because it "didn't have the operational impact [the NSA] needed," according to NSA chief Gen. Keith Alexander.

"That was a choice that came from us, from NSA," he said today at the Armed Forces Communications and Electronics Association's International Cyber Symposium in Baltimore.

Alexander insisted that NSA did not keep what it had collected before the program ended and that "all that data was purged at that time."

The event at which Alexander spoke was sponsored by communications behemoth Verizon and defense contractor Booz Allen Hamilton. Snowden was a Booz contractor at the NSA and swiped a secret FISA court order directed at Verizon Business Services regarding agency collection of phone metadata from callers both inside and outside the U.S., which was the first leak published by the Guardian this month.

U.S. diplomats, meanwhile, continue to press authorities in Russia – which has no extradition agreement with the U.S., though the two countries do exchange captured fugitives – to send Snowden home to face charges under the 1917 Espionage Act.

"We'd like to see him come home," State Department spokesman Patrick Ventrell said in Washington.

And while some supporters, like Pentagon Papers leaker Daniel Ellsberg, call Snowden a hero for exposing the secret surveillance programs, others, like Secretary of State John Kerry, have said he's putting American lives at risk.

Al Qaeda and its affiliates have been reading the leaked documents and advising violent jihadis to take actions to avoid electronic surveillance by the NSA, a senior U.S. intelligence official told ABC News.

READ: In Their Own Words, Is Edward Snowden a Hero or a Traitor?

ABC News' Kirit Radia, Luis Martinez, Akiko Fujita and Natalia Osipova contributed to this report.