The US regulator said action by Brussels would make it into a "supra-national tax authority" overriding the tax codes of its member states.
The commission is investigating a tax deal Apple was granted for setting up headquarters in Ireland.
The EC said it was trying to ensure EU law was applied indiscriminately.
The investigation could result in a billion pound tax bill for Apple.
Apple has been accused of sheltering billions of pounds in profit in the Republic of Ireland tax-free, under a deal, it reached with Dublin.
The EC investigation could result in a billion pound tax bill for Apple.
Apple is not the only company to face scrutiny over its tax deals. The European Commission has been looking into several instances of tax avoidance, mainly targeting US companies.
The commission said it was investigating whether Apple was given a special tax benefits for setting up in Ireland that were not granted to other companies, potentially violating EU state aid rules.
The US regulator said that Brussels was using a different set of criteria to judge cases involving US companies than it has used in past investigations and called the potential action "deeply troubling".
Earlier this year the US government publicly challenged the investigation by Brussels accusing it of targeting US corporations.
In its latest move, the Treasury Department issued a white paper on Wednesday asking Brussels to reconsider its actions against several US companies including Apple, Starbucks, and Amazon. It argued penalties on for these firms could have broader repercussions for cross-border taxation carefully.
"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 on agencies website.
It argued that a charge from the European Commission on US corporations back taxes could be considered a foreign tax credit in the US - a classification that could reduce the businesses US tax bill significantly possibly wiping it out entirely.
The Treasury Department said it was continuing to "consider potential responses should the Commission continue its present course".
In response the EC said there was no bias against US companies and that it was trying to ensure EU law was applied indiscriminately to all companies operating in Europe.