Reports suggest the income came from iTune sales
Apple has been ordered to pay some 12 billion yen (€105m) in tax after under-reporting income in Japan - according to NHK, Japan's largest broadcasting organisation.
It reports that the amount has now been paid in full.
The shortfall is believed to have related to profits earned from Japanese payments to Apple's iTunes unit - profits from the unit were transferred to Apple's Irish operation.
Apple is yet to comment on the reports which come on the same day that its new flagship iPhone 7 range goes on general release.
The company has been ordered to pay some €13bn in back taxes in Ireland after the European Commission ruled that the company received illegal state aid. Both Apple and the Irish Government have disputed this finding.
Meanwhile, the Obama administration has moved to limit the use of foreign tax credits by US multinational companies to reduce their tax bills at home.
The US Treasury confirmed that it was tightening restrictions on these credits on Thursday, the current rules could lead to the US exchequer taking a significant hit as a result of Apple's tax payments.
The US taxes companies on all of their global income - while offering dollar-for-dollar tax credits to offset payments made in other territories. This could result in a €13bn ($14.6bn) loss to the corporate tax take in the US if Apple is ultimately required to pay these back taxes.