Increasingly ubiquitous encryption has created a “serious problem” for law enforcement deserving of debate, said the Justice Department’s second-in-command.

Rod Rosenstein, President Trump’s deputy attorney general, addressed the repercussions of impenetrable encryption during an appearance Wednesday afternoon at a cybersecurity conference in Boston where he reiterated his concerns about law enforcement’s growing inability to decipher digital communications — a phenomenon the FBI has labeled “going dark.”

While investigators have wrestled for years with the dilemma, Mr. Rosenstein told attendees the factors including increasingly secure smartphones and the rise of instant-messaging programs that encrypt messages by default have created an environment that “threatens to destabilize the constitutional balance between privacy and security that has existed for over two centuries,” according to a copy of his prepared remark released by the Justice Department.

“We in law enforcement have no desire to undermine encryption. But the advent of ‘warrant-proof’ encryption is a serious problem,” Mr. Rosenstein said, according to the transcript.

“Our society has never had a system where evidence of criminal wrongdoing was totally impervious to detection, even when officers obtain a court-authorized warrant. But that is the world that technology companies are creating,” Mr. Rosenstein added.

Authorities raised such concerns throughout the Obama administration, but the problem was propelled front and center in December 2015 after investigators recovered a password-protected Apple iPhone from the scene of a 2015 mass shooting in San Bernardino, California.

The Justice Department sued Apple in federal court the following year in hopes of compelling the company’s assistance with accessing the phone’s contents, but Apple relented and the government ultimately hired an undisclosed third party to hack the device.

Mr. Trump called for boycotting Apple when the company initially challenged the government’s request but hasn’t explicitly addressed the issue during his nine months in the White House.

“We should have a candid public debate about the pros and cons of allowing companies to create lock boxes that cannot be opened by police and judges,” Mr. Rosenstein said Wednesday.

Former FBI Director James Comey told members of Congress in May that encryption prevented authorities from gleaning digital evidence from roughly 46 percent of the approximately 3,000 smartphones other electronic devices seized by criminal investigators during a recent six-month span.

“That means half of the devices that we encounter in terrorism cases, in counterintelligence cases, in gang cases, in child pornography cases, cannot be opened with any technique,” Mr. Comey told the Senate Judiciary Committee. “That is a big problem. And so the shadow continues to fall.”

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