Microsoft Corp. and Verizon Communications Inc. have faced new setbacks in their battles against the collection of customer information by U.S. authorities, leaving the U.S. government with the upper hand, according to court documents and news reports published Friday.

In the U.S. District Court for the Southern District of New York, U.S. Magistrate Judge James Francis IV rejected Microsoft’s argument that the government can obtain only customer emails Microsoft stores in the United States, not abroad. And in the Foreign Intelligence Surveillance Court, Judge Rosemary Collyer declassified a March 20 order [PDF] that denied an unidentified telephone company’s challenge against the National Security Agency’s bulk collection of customer data from telecommunications businesses. The Washington Post reported the company is Verizon.

Microsoft is seeking to stop a search warrant by an unnamed federal agency for a customer’s emails, the content of which is on a server in Dublin. Francis wrote in his order the company’s argument against the warrant was “simple, perhaps deceptively so.”

David Howard, corporate vice president and deputy general counsel at Microsoft, wrote in a blog post that the order by Francis hasn’t deterred the company.

“This is the first step toward getting this issue in front of courts that have the authority to correct the government’s longstanding views on the application of search warrants to content stored digitally outside the United States,” Howard wrote. “While the law is complicated, the issue is straightforward. It’s generally accepted that a U.S. search warrant in the physical world can only be used to obtain materials that are within the territory of the United States.”

As for Verizon, the company in January received from the FISA court an order requiring it to turn over data on customers’ phone calls. But Verizon fought the demand [PDF], pointing to U.S. District Judge Richard Leon’s December ruling in which the federal judge in Washington, D.C., concluded that the government’s bulk collection of phone records “almost certainly” violated Americans’ constitutional privacy rights.

Collyer wrote in her order that she disagreed with Leon, noting “the noncontent telephony metadata at issue here is particularly limited in nature and subject to strict protections that do not apply to run-of-the-mill productions of similar information in criminal investigations.”

A Verizon representative didn’t immediately respond to requests for comment.