The Pentagon has awarded a $10bn (£8bn) cloud-computing contract to Microsoft, following a heavily-scrutinised bidding process in which Amazon had been seen as the favourite.
The 10-year contract for the Joint Enterprise Defence Infrastructure, or Jedi, is aimed at making the US defence department more technologically agile.
Amazon's bid drew criticism from its rivals and US President Donald Trump.
The company on Friday said it was "surprised" by the decision.
A "detailed assessment purely on the comparative offerings" would "clearly lead to a different conclusion", it said.
In its statement, the Pentagon said all offers "were treated fairly".
The Department of Defense wants to replace its ageing computer networks with a single cloud system.
Under the contract, Microsoft will provide artificial intelligence-based analysis and host classified military secrets among other services.
It is hoped that Jedi will give the military better access to data and the cloud from battlefields.
Amazon had been considered the front-runner - until President Trump began questioning whether the process was fair.
In July he told reporters that he was getting "tremendous complaints about the contract with the Pentagon and Amazon".
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