Following a lengthy bidding process and accusations of conflict of interest, software titan Microsoft has been awarded the coveted ten-year $10bn (£8bn) could-computing contract for the Joint Enterprise Defence Infrastructure (JEDI).

Amazon, thought to be the favourite, has expressed surprise at the decision. Amazon’s lucrative bid was met criticism from its rivals and US President Donald Trump, who said in August his administration was reviewing the bid after complaints from other firms.

At the time, Trump told the press he was getting “tremendous complaints about the contract with the Pentagon and Amazon” and that companies had told him the contract “wasn’t competitively bid”.

Amazon responded to the decision saying that a “detailed assessment purely on the comparative offerings” would “clearly lead to a different conclusion”. The online retailer is currently evaluating its options for protesting the award.

Microsoft executive Toni Townes-Whitley said the company was “proud” to have had its cloud technologies picked by the Department of Defense to “satisfy the urgent and critical needs of today’s warfighters”.

The move is likely to boost Microsoft’s share price and bring hugely positive financial implications for the company over the coming years.

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In its statement, the Pentagon said: “All (offers) were treated fairly and evaluated consistently with the solicitation’s stated evaluation criteria. Prior to the award, the department conferred with the DOD Inspector General, which informed the decision to proceed”.

The announcement follows just days after Defence Secretary Mark Esper removed himself unexpectedly from the review process after months of involvement, on the basis one of his sons worked for IBM.

Concerns were raised that a single award could potentially give the winner an unfair advantage in follow-on work.

JEDI is a key part of the Pentagon’s decision to move much of its computing power online, it will enable the US defence department to replace its ageing computer network with a single cloud system. Under the contract, Microsoft will provide artificial intelligence (AI) based analysis and host classified military secrets among other services.

It forms part of a wider movement by the department towards modernisation and to make it more technologically agile. One of the main goals of the project is to provide the military with better access to data and the cloud from remote locations and battlefields.

According to many officials, the department’s systems are painfully outdated and they are unable to access files or share information as fast as they might be able to in the private sector.