In a statement, a spokesman for Amazon Web Services said "Numerous aspects of the JEDI evaluation process contained clear deficiencies, errors, and unmistakable bias -- and it's important that these matters be examined and rectified."
The Pentagon announced the contract award last month.
U.S. Defense Secretary Mark Esper said Friday he was certain that the award of the contract to Microsoft instead of Amazon was done fairly.
Esper recused himself from the contract decision because his son had worked for one of the other unsuccessful bidders.
"I am confident that it was conducted freely and fairly without any type of outside influence," Esper said at a news conference in Seoul, South Korea, the Associated Press reported.
Amazon dominates the cloud computing space with about 33% of the business, while Microsoft trails with about 16%.
Donald Trump called for a review of the contract process last summer as incoming Esper took office. At the time, many pundits were expecting Amazon to win the deal.
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