The European Commission in Brussels was given 10 months to draw up new figures by the Luxembourg-based Euyropean Court of Justice.
The ruling came in a case brought by a number of companies including Esso and Dow against national authorities in Italy, the Netherlands and Austria.
"The court declares invalid the maximum annual amount of free allowances for greenhouse gas emissions determined by the Commission for the period 2013-2020," the court said in a statement.
The EU's Emissions Trading System (ETS), the world's largest, puts a cap on carbon dioxide emitted by large factories and other companies.
The firms can trade in quotas of these emissions -- the idea being to provide a carrot to improve energy efficiency or switch to cleaner sources so that they keep within the ceiling.
A large part of the quotas are free, partly to help European companies against international competitors.
