"I trust it was done freely and fairly, without any external influence," Esper said at a press conference in Seoul and noted that he had refused the cloud computing contest.
Amazon says the policy interfered with the fair hiring process. President Donald Trump has criticized Amazon and its founder Jeff Bezos for a long time.
At a company meeting on Thursday, Amazon Web Services CEO Andy Jassy said it would be difficult for an American agency to grant a contract objectively when the president denigrates one of the applicants, according to a company spokesman. .
Amazon was considered the favorite to keep the contract, part of a broader digital modernization process of the Pentagon, before Microsoft emerged as the surprise winner.
In October, Esper refused to review the agreement because his son was hired with IBM Corp, one of the original applicants for the contract. IBM had applied for the contract, but had already been eliminated from the competition.
Esper said he was not aware of Amazon's specific accusations. His comments answered a question about whether Trump asked the Pentagon to "avoid Amazon" for the contract.
The challenge to the Department of Defense's decision announced last month was expected by experts, analysts and consultants, especially after Trump publicly mocked Amazon's bid for the contract.
Trump had said in August that Amazon's application for the Joint Enterprise Defense Infrastructure Cloud (JEDI) defense infrastructure contract was under review by its government following complaints from other companies.