"It's total political crap," Cook told the Irish Independent newspaper, of European Competition Commissioner Margrethe Vestager's assertion that the company had paid a tax rate of 0.005 percent on its European profits in 2014.
The commission ruled that Apple had received favourable tax terms that amounted to state aid -- illegal under its rules.
Cook earlier told Irish national broadcaster RTE that Apple had never received any "sweetheart deal" from Ireland and that his company's global tax rate in 2014 was 21.6 percent.
The tech boss called on Irish government ministers to "do the right thing" when they meet Friday and approve an appeal against the ruling.
Finance Minister Michael Noonan said he would seek official cabinet approval for an appeal hours after the decision was delivered Tuesday, describing it as "bizarre".
However, an emergency cabinet meeting of Ireland's minority government on Wednesday failed to agree, with some ministers demanding a parliamentary vote on the issue.
"We have been committed to Ireland for 37 years; we have had a long-term romance together and I'm pretty confident the government will do the right thing and I think the right thing here is to stand up and fight," Cook told RTE, speaking from California.
Apple will appeal and Cook believes Ireland will do the same in the interests of protecting future inward investment.
He also criticised the retrospective nature of the order, which covers alleged unpaid taxes from 1993-2001.
"It's like playing a sports game and winning the championship and then finding out the goals are worth less than you thought they were," he told RTE.
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