Amazon Web Services on Friday confirmed that it has filed a lawsuit challenging the Defense Department's decision to award Microsoft a major contract for cloud services.

The JEDI (Joint Enterprise Defense Infrastructure) deal, which could be worth up to $10 billion, was hotly contested and marks a big win for Microsoft as it chases down AWS in cloud infrastructure.

The high-profile process was controversial because President Trump got personally involved, expressing opposition to awarding the contract to Amazon, whose CEO, Jeff Bezos, has been a target of Trump's attacks as owner of the Washington Post. Amazon has submitted videos of Trump to the Court of Federal Claims, which is handling the bid protest. The complaint itself is not publicly accessible.

"The Complaint and related filings contain source selection sensitive information, as well as AWS's proprietary information, trade secrets, and confidential financial information, the public release of which would cause either party severe competitive harm," Amazon told the court in a filing, while seeking a protective order. "The record in this bid protest likely will contain similarly sensitive information."

The Pentagon announced that Microsoft had won the contract on October 25. Soon after, Amazon said it was surprised that Microsoft had received it. Amazon announced plans to protest the award last week and said that the process had contained biases and mistakes.

"We have confidence in the qualified staff at the Department of Defense, and we believe the facts will show they ran a detailed, thorough and fair process in determining the needs of the warfighter were best met by Microsoft," a Microsoft spokesperson told CNBC in an email on Friday.

IBM and Oracle had also sought to win the contract but were removed from consideration.

The case has been assigned to Judge Patricia Elaine Campbell-Smith. Amazon said in a filing that assigning the case to another judge on the court, Eric Bruggink, "would conserve judicial resources and promote the efficient administration of justice" because Bruggink ruled on a bid protest over JEDI that Oracle filed last year. That case is now before the U.S. Court of Appeals for the Federal Circuit.

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