There has been widespread criticism in the US of the European Commission's ruling that Apple should pay up to €13bn in back taxes.
The US Treasury said that such tax investigations were "unfair" and a senior Democrat senator called the move a "cheap money grab".
White House spokesman Josh Earnest said if Apple paid the back taxes, it might offset that amount against tax due in the United States, which would be unfair for American taxpayers.
The European Commission said Ireland had enabled Apple to pay substantially less than other businesses, in effect paying a corporate tax rate of no more than 1 percent.
Apple and the government of Ireland plan to appeal against the record penalty.
"Member states cannot give tax benefits to selected companies - this is illegal under EU state aid rules," said Competition Commissioner Margrethe Vestager.
The standard rate of Irish corporate tax is 12.5 percent. The Commissions's investigation concluded that Apple had effectively paid 1 percent tax on its European profits in 2003 and about 0.005 percent in 2014.
The US Treasury said retroactive tax assessments by the Commission were "unfair, contrary to well-established legal principles, and call into question the tax rules of individual member states."
Last week the Treasury warned that the European Commission was in danger of becoming a "supranational tax authority".
Charles Schumer, one of the highest-ranking Democratic senators, said: "This is a cheap money grab by the European Commission, targeting US businesses and the US tax base."
"By forcing their member states to retroactively impose taxes on US companies, the EU is unfairly undermining our ability to compete economically in Europe while grabbing tax revenues that should go toward investment here in the United States," he said.
Apple said the decision would be harmful for jobs.
"The European Commission has launched an effort to rewrite Apple's history in Europe, ignore Ireland's tax laws and upend the international tax system in the process," the company said.
"The Commission's case is not about how much Apple pays in taxes, it's about which government collects the money. It will have a profound and harmful effect on investment and job creation in Europe.
"Apple follows the law and pays all of the taxes we owe wherever we operate. We will appeal and we are confident the decision will be overturned."
The Irish government held a similar view, with finance minister Michael Noonan saying: "The decision leaves me with no choice but to seek cabinet approval to appeal. This is necessary to defend the integrity of our tax system; to provide tax certainty to business; and to challenge the encroachment of EU state aid rules into the sovereign member state competence of taxation."
However, the record tax bill should not be a problem for Apple, which made a net profit of $US53 billion in the 2015 financial year.
Apple is not the only company that has been targeted for securing favourable tax deals in the European Union.
Last year, the commission told the Netherlands to recover as much as €30m from Starbucks, while Luxembourg was ordered to claw back a similar amount from Fiat.