Ryanair has added an extra 25p to every booking to cover the cost of the new Emissions Trading Scheme (ETS) fee.
The company said the charge will be implemented from 17 Tuesday, to help cover the cost of the new 'green' tax, which will be around £16.5 million.
According to the Express, the ETS will require airlines to buy credits for their greenhouse gas emissions.
The ETS scheme has come under fire from airlines as well as passengers, who are already charged the highest Air Passenger Duty in Europe.
Ryanair spokesman Stephen McNamara said: "This latest EU stealth tax will damage traffic, tourism, European competitiveness and jobs at a time when no other economic block is including aviation in their ETS schemes."
The Daily Mail reports that ETS will cost Ryanair passengers between 15 million and 20 million euros in 2012.
The news comes after China revealed it refuses to pay the ETS levy, although the EU insists it will not back down, and any airline who does not comply will be find or even banned from flying in the European Union.