State-owned South African Airways (SAA) will increase prices on all European flights to offset the costs of the EU's Emission Trading Scheme, it said on Monday.
The national flag carrier said it would increase fuel surcharges on flights to and from Europe by between 1 and 2 euros per passenger from July 1.
Europe has angered trading partners with its plan to make airlines cut pollution by levying a fee based on the amount of carbon emissions calculated for entire flights, not just the portion over Europe - a measure its critics regard as interference with their national airspace.
Since the start of this year, all airlines using European Union airports are required to buy permits under the ETS, drawing protests from around the world with China banning its carriers from taking part.
"We are doing this under protest," said Siza Mzimela, chief executive of SAA.