The European Union executive also cut the Czech Republic's proposed cap by 14.8 percent, while it accepted the emissions limits proposed by France. The Commission set Poland's cap at 208.5 million tonnes per year, down 26.7 percent from the government's proposal. The Polish plan is the third-largest that the EU executive has ruled on for the second phase of the emissions trading scheme.
Poland said it would not accept the decision, charging that the move would hurt economic development and energy security.
The Czech Republic's limit was set at 86.8 million tonnes per year. France's cap was accepted at 132.8 million tonnes per year.
The EU's emissions trading scheme sets limits on the amount of CO2 big factories such as power plants and oil refineries can emit. Companies that exceed their limits can buy permits, while those that come in below can sell them.
The emissions trading scheme is the 27-nation EU's key tool to fight climate change and meet commitments to cut emissions under the Kyoto Protocol.
(Additional reporting by Darren Ennis and Natalia Reiter)