In a white paper commissioned by US Treasury secretary Jack Lew, the Obama administration warned that Brussels was overstepping its powers and becoming a "supranational tax authority", The Guardian reported on Thursday.
The EU is investigating whether Apple's tax deals with Ireland running into as much as $19 billion for alleged unpaid taxes.
The EU is also probing Amazon and Starbucks over allegations of tax avoidance.
"The investigations have global implications as well for the international tax system and the G20's agenda to combat (tax avoidance) while improving tax certainty to fuel growth and investment," Robert Stack, a Treasury Department deputy, wrote in a blog post.
According to the white paper, the EU investigations could "create an unfortunate international tax policy precedent".
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