French magazine L’Express reported that the firm paid nearly €500m ($570m, £439m) in a confidential settlement reached late last year.
Apple’s French business confirmed there was a deal in a statement to the Reuters news agency but refused to say how much was paid.
France is lobbying for an EU-wide tax on the biggest technology firms.
“As a multinational company, Apple is regularly audited by fiscal authorities around the world,” Apple France said in the statement.
“The French tax administration recently concluded a multi-year audit on the company’s French accounts, and those details will be published in our public accounts.”
L’Express reported that the investigation centred on the small amount of sales the firm booked in France despite the size of France as a market for Apple.
Most of its sales are booked in Ireland where the US firm has its European headquarters, and which has a low corporate tax rate.
Last year Apple paid an extra £136m in tax following an “extensive audit” by HM Revenue and Customs.
Apple Europe agreed to pay a “corporate income tax adjustment” covering years up to 26 September 2015.
In September, Ireland said it had recovered $13.1bn in disputed taxes from Apple plus interest of €1.2bn which it will hold in anticipation of its appeal against an EU tax ruling.