AWS lost the prestigious Cloud contract on October 25 that will provide enterprise level, commercial Infrastructure as a Service (IaaS) and Platform as a Service (PaaS) to support Department of Defence business and mission operations.
Even Microsoft was somewhat caught off-guard by the DoD announcement.
In a statement to ZDNet, an AWS spokesperson said "We believe it's critical for our country that the government and its elected leaders administer procurements objectively and in a manner that is free from political influence".
"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 spokesperson added.
In August, the Pentagon said it was putting the JEDI contract on hold after US President Donald Trump complained about potential conflicts of interest in the process.
Bezos has often been targeted by the US President because of his ownership of The Washington Post and the views of the paper against the Republicans.
The Pentagon selected Microsoft and AWS as the two finalists for its $10 billion Cloud contract, as earlier contender Oracle missed the bus.
The JEDI Cloud computing contract is aimed to bring the entire military under the envelope of a single Cloud provider.
Trump, who has been a critic of Amazon and Bezos over the company's tax arrangements, even got involved during the bidding process, saying the government was looking at the contract after "getting enormous complaints" from competitors to Amazon and Microsoft.
US Defense Secretary Mark Esper, however, rejected any notion of bias in a decision to award Microsoft the JEDI contract.
"I am confident it was conducted freely and fairly, without any type of outside influence," he told a news conference in Seoul on Friday.