The US Treasury Department has warned the European Commission about taking action against US companies over tax avoidance allegations.
The commission is investigating tax deals granted to US companies for setting up headquarters in Europe.
Next month the EU is expected to deliver its decision on Apple. The company could be hit with a multi-billion pound bill for unpaid taxes.
The commission said there was “no bias against US companies” in the probes.
In a report published on wednesday, the US regulator said action by Brussels would make it into a “supra-national tax authority” overriding the tax codes of its member states.
It also said Brussels was using a different set of criteria to judge cases involving US companies, adding that potential penalties were “deeply troubling.”
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Apple has been accused of sheltering billions of pounds in profit in the Republic of Ireland tax-free, under a deal it reached with Irish authorities. JP Morgan, an investment banker for Apple, has said the company could face a bill for $19bn (£14.3bn) in a worst-case scenario.
Several companies including Apple, Amazon and Starbucks are under investigation by the European Commission over allegations of tax avoidance.