Apple has been ordered to pay about 12bn yen (£89m) in taxes for improperly reporting income associated with its Japan iTunes unit, according to reports.

The news comes weeks after the EU hit Apple with a record £11bn tax penalty, ruling its 25-year “sweetheart deal” with Ireland was illegal.

Apple’s unit in question has reportedly paid the amount that was asked by the Tokyo Regional Taxation Bureau.

The tax authority argued that the iTunes unit, which sends parts of its profits earned from fees paid by Japanese subscribers to another Apple unit based in Ireland, had not been paying a withholding tax on these earnings in Japan, according to local broadcaster NHK.

It was not immediately clear when the bureau issued the penalty or when Apple agreed to pay it, and the tech giant did not respond to a request for comment.

The EU has been a strong critic of multinational companies such as Apple, Starbucks and Fiat Chrysler that have benefited from keeping their money overseas.

The move allows these companies to avoid paying hefty taxes they could face by bringing the money back to the US.

EU orders Apple to pay up to 13 billion euros tax to Ireland

European Commissioner Margrethe Vestager, in charge of competition policy said that EU member states cannot give tax benefits to selected companies, after Apple was ruled to pay £11bn in tax to Ireland last month. “This is illegal under EU state aid rules. The commission’s investigation concluded that Ireland granted illegal tax benefits to Apple, which enabled it to pay substantially less tax than other businesses over many years,” she said.

“In fact, this selective treatment allowed Apple to pay an effective corporate tax rate of 1 per cent on its European profits in 2003 down to 0.005 per cent in 2014.”

Tim Cook, Apple’s chief executive, said the Ireland tax ruling was “total political crap” and “maddening”.

10 of the biggest tax havens in the world Show all 10 1 /10 10 of the biggest tax havens in the world 10 of the biggest tax havens in the world Luxembourg There are an estimated £2.5 trillion shares of mutual funds registered in the Grand Duchy, £1 trillion of which cannot be traced to an owner 10 of the biggest tax havens in the world Cayman Islands The Cayman Islands contain 6% of the world's total banking assets, but just 0.000008% of its population 10 of the biggest tax havens in the world Isle of Man David Cameron has said the Isle of Man, where there is no corporation, capital gains or inheritance tax, should not be considered a tax haven 10 of the biggest tax havens in the world Jersey There are over £3.5 billion assets per square mile on the self-governing Channel Island 10 of the biggest tax havens in the world Ireland Ireland made headlines last year when it emerged Apple was registered in the country in order to dodge over £40bn in taxes 10 of the biggest tax havens in the world Mauritius The Mauritian government notionally charges corporation tax, but companies can easily make this back through generous tax credits for foreign businesses 10 of the biggest tax havens in the world Bermuda Google holds more than £30bn in offshore cash reserves, primarily via Bermuda 10 of the biggest tax havens in the world Monaco A popular domicile for super-rich private individuals, Monaco has the most expensive property in the world. £1 million will buy just 225 square feet 10 of the biggest tax havens in the world Switzerland Switzerland has such secretive banking laws that it took until the 1990s to secure the release of Nazi cash reserves 10 of the biggest tax havens in the world Bahamas David Cameron's father ran an offshore fund which hired Bahamas residents to complete paperwork, thus dodging British tax bills

Apple and Dublin plan to appeal the ruling, arguing the tax treatment was in line with EU law.