Bloomberg reported that the malicious chips were planted by a unit of the Chinese People's Liberation Army, which infiltrated the manufacturing supply chain of American server supplier Super Micro Computer (Supermicro).
In its lengthy statement, Amazon said: "We've found no evidence to support claims of malicious chips or hardware modifications". In addition to large U.S. companies, the motherboards also were used by Defense Department data centers and Central Intelligence Agency drone operations.
The story cited 17 unnamed sources, including industry insiders and current and former USA officials.
Amazon and Apple have both strongly denied the results of the investigation.
Bloomberg claims the probe led to some companies removing servers made by Super Micro and ending business relationships with the company.
Apple took Bloomberg to task, saying the agency had contacted it "multiple times with claims, sometimes vague and sometimes elaborate, of an alleged security incident".
"Nested on the servers' motherboards, the testers found a tiny microchip, not much bigger than a grain of rice, that wasn't part of the boards' original design", according to the Bloomberg report.
The Bloomberg News report said the chips, the size of a grain of rice, were used on equipment made for Amazon, which first alerted USA authorities, and Apple, and possibly for other companies and government agencies.More news: Why Arsenal u-turned deal with Ramsey
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The tech giant further stated that it was "accidental" and was not a "targeted attack against Apple".
Supermicro's customers include Elemental Technologies, a streaming services startup which was acquired by Amazon in 2015 and provided the foundation for the expansion of the Amazon Prime Video platform.
"While we would cooperate with any government investigation, we are not aware of any investigation regarding this topic nor have we been contacted by any government agency in this regard", Super Micro's statement said. The Chinese government did not address the report.
An Apple spokesperson said: "We are deeply disappointed that in their dealings with us, Bloomberg's reporters have not been open to the possibility that they or their sources might be wrong or misinformed".
The attack by Chinese spies reached nearly 30 US companies by compromising America's technology supply chain, according to extensive interviews with intelligence and corporate sources.
Many more details are in Bloomberg's report. Apple never had any contact with the Federal Bureau of Investigation or any other agency about such an incident. It's not clear what, if anything, China has gleaned from the operation, though the story says no consumer information is believed to have been stolen. The report alleges that data center hardware purchased from a Chinese company called Supermicro included Chinese spy chips that put the security of the networks at risk.
The FBI and the Office of the Director of National Intelligence, representing the CIA and NSA, declined to comment to Bloomberg. Apple and AWS deny these moves involving Super Micro were related to chip worries.