The U.S. government’s overly broad use of secret warrants to search digital files belies President Obama’s transparency pledge. Microsoft is right to challenge this practice.

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THERE were high hopes for transparency from President Obama, a former constitutional law professor who pledged to create “an unprecedented level of openness” in government.

Reviews of his progress on this front have looked at his limited press availability, public disclosures and crackdowns on whistleblowers.

Another measure is his administration’s deeply troubling use of secrecy to obscure government searches of private documents and communication.

Unless policy or rule changes are made soon, one of Obama’s legacies will be untold search warrants sealed forever, with permanent gag orders preventing citizens and companies from ever knowing whether his administration snooped through their messages, photos and digital files.

Microsoft is challenging this practice by suing the U.S. Department of Justice — its past nemesis — for violating the First and Fourth amendments of the U.S. Constitution. It’s the company’s fourth lawsuit against the government to bring more transparency over its clandestine practices.

The Redmond company is protecting its interests — its success depends on people trusting the security of its products. But it’s also waging a noble fight to update and rein in overly aggressive surveillance policies that undermine America’s fundamental values.

By serving secret warrants on cloud-service companies, the government avoids notifying individuals and businesses that it’s searching their files.”

As of last week, 90 signatories were supporting Microsoft’s suit, including national business and journalism organizations, former federal prosecutors, privacy advocates, Amazon, Google and media outlets, including The Seattle Times.

By serving secret warrants on cloud-service companies, the government avoids notifying individuals and businesses that it’s searching their files. Gag orders are used to prevent cloud companies from notifying customers of the intrusion, often forever.

As Microsoft said in its filing, the government “has exploited the transition to cloud computing as a means of expanding its power to conduct secret investigations.”

So civil liberties are being lost as people and businesses transition from storing their digital files locally to an online service.

Muzzling cloud companies violates their First Amendment rights. Perpetually secret warrants violate the Fourth Amendment, which protects privacy by prohibiting unreasonable searches and requiring warrants that disclose what’s being searched.

Fixing this problem would not jeopardize investigations that need temporary secrecy; nobody is saying they should be prohibited.

The issue is whether the government is overreaching in its secrecy, a tool that’s supposed to be used in limited circumstances. Instead, secrecy orders, issued secretly by courts, are being used to permanently cloak what the government is doing, and has done, to its citizens.

In the 18 months before the suit was filed in April, courts forced Microsoft to keep secret 2,576 legal demands. More than two-thirds had no fixed end date, meaning Microsoft can never inform affected companies or individuals that their privacy was breached and the government searched their digital file cabinets. And Microsoft’s just one of the major cloud companies.

In addition to violating the Constitution, this secrecy makes it impossible for the public to hold its government accountable. Were searches justified and worthwhile? Who knows?

Security and law enforcement are important, of course. But they can’t be used as excuses to abandon America’s core values.

Congress can make fixes when it updates the Electronic Communications Privacy Act. An update was approved by the U.S. House in April and is pending in the Senate.

The DOJ could also create a policy itself, setting more limits on secrecy, and help President Obama get closer to one of his initial policy goals.