Qantas Airways claims the new carbon tax is likely to increase the cost of its operations by as much as 115m Australian dollars ($122m; £76.7m).
However, the airline says the extra cost will be passed on to passengers as it increases fares.
Qantas expects the price on a single domestic flight to rise by about A$3.50 in 2013.
The Australian government has unveiled plans to impose a tax on carbon emissions in the country.
Prime Minister Julia Gillard said carbon dioxide emissions would be taxed at A$23 per tonne from 2012.
