(Bloomberg) -- After buying a software tool to access a dead terrorist’s encrypted iPhone, the FBI is exploring how to make broader use of the hack while bracing for a larger battle involving encrypted text messages, e-mails and other data, Director James Comey said.

The tool used to get into the phone used by Syed Rizwan Farook, who with his wife carried out a deadly December attack in San Bernardino, California, could "in theory be used in any case where there’s a court order" to access data on an iPhone 5c running Apple’s iOS 9 operating system, Comey told reporters in Washington on Wednesday.

However, accessing content on a phone -- known as “data at rest” -- is only part of the challenge that encryption poses for U.S. investigators. Software applications and other services that encrypt texts, e-mails and other information in transit over the Internet -- known as “data in motion” -- are “hugely significant,” especially for national security investigations, Comey said.

"The data at rest problem affects non-national security law enforcement overwhelmingly," Comey said. "The data in motion, at least today, overwhelmingly affects our national security work. Terrorists and their fellow travelers are increasingly using end-to-end encrypted apps."

Comey said criminals are increasingly using services that encrypt data in motion, and he didn’t rule out litigation against companies such as Facebook Inc.’s mobile messaging service WhatsApp, which has more than 1 billion subscribers worldwide.

WhatsApp has been embroiled in a legal dispute in Brazil, with judges twice in the last six months temporarily ordering the service blocked for failing to turn over data in response to court orders. A Facebook executive in Brazil also was detained in March for allegedly failing to cooperate with orders.

"WhatsApp has over a billion customers, overwhelmingly good people," Comey said. "But in that billion customers are terrorists and criminals, and so that now ubiquitous feature of all WhatsApp products will affect both sides of the house."

Comey said he currently doesn’t have plans to bring a legal case against WhatsApp. "Whether there will be litigation down the road, I don’t know," he said.

Hacking Tool

The FBI served Apple with a court order in February compelling the company to help break into an encrypted iPhone used by Farook. Apple resisted, and the FBI dropped the case last month after saying it bought a tool from a private entity it hasn’t identified to break into the phone.

State and local law enforcement agencies say they have hundreds of encrypted iPhones that they could use the FBI’s help getting into.

From October 2015 to March of this year, New York City police have been locked out of 67 Apple devices lawfully seized during investigations into 44 violent crimes, including murders, rapes and the shootings of two officers, Thomas Galati, chief of the New York City Police Department’s intelligence bureau, told a House Energy and Commerce subcommittee last month.

The FBI is trying to figure out how to allow "law enforcement around the county with court orders to be able to use our tool," Comey said. 

It’s "tricky," he said, because using the tool to help state and local criminal investigations could mean that it would have to be revealed in a court proceeding if there isn’t a procedure in place to prohibit testimony about how it works.

"If we use it in a criminal case in such a way that it becomes a feature of litigation, then the nature of the tool may be exposed and it’s utility may be significantly decreased," Comey said.

"I expect in the near future we’ll have figured out how we’re going to do it," he said. "Then we’ll tell local law enforcement, ‘If you send us a phone here are the rules.’"

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