Apple has been ordered to pay about 12 billion yen ($118m; £89m) in taxes for improperly reporting income associated with its Japan iTunes unit, according to local reports.
The news comes a few weeks after the EU hit Apple with a record €13 billion (£11 bn) 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 Taxation Bureau.
The regional tax authority argued that the iTunes unit send parts of its profits, earned from fees paid by Japanese subscribers, to another Apple unit based in Ireland. However, this unit had not been paying a withholding tax on these earnings in Japan, Reuters reported citing local broadcaster NHK.
It was not immediately clear when the bureau issued the penalty or when Apple agreed to pay it. Apple did not immediately respond to a request for comment from the Independent.
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.
Commissioner Margrethe Vestager, in charge of competition policy, said: “Member States cannot give tax benefits to selected companies – 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.
“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 chief executive, said the EU commission ruling that Apple should pay €13 billion over its tax arrangements in Ireland is “total political crap” and “maddening”.
Ryanair boss, Michael O’Leary also waded into the debate earlier this month, saying the Irish government should tell the EU to “f**k off”.
Apple and Dublin plan to appeal the ruling, arguing the tax treatment was in line with EU law.
Theresa May's new government has fuelled the debate over tax avoidance saying it would "welcome any company" to the UK just hours after the EU announced the Apple decision. In a statement Number 10 and the Treasury said that Britain should "remain open for business", in the wake of the Brexit vote.
