The allocations, delayed since early last year, will mean more supply hitting an already oversupplied market and could exert downward pressure on carbon prices that have fallen 9 percent this week.
Bulgaria, Croatia, Cyprus, Italy, Poland, Romania and Spain, representing a total 272.6 million allowances, were the last countries to be given approval by the Commission, it said in a statement on its website.
Industrial firms regulated by the EU Emissions Trading System will get a total of 6.6 billion free allowances between 2013 and 2020, including 887 million for last year, to help them compete with rivals in other countries that have looser environmental regulations.
Companies have traditionally received their annual allocation in February, but this was delayed last year largely due to late submissions by governments following a change in the process at the start of the new eight-year trading phase.
The Commission also said several countries have begun to give out their free permits for 2014. Britain, the EU's second largest emitter, said earlier this week it has started awarding its 2014 permits to firms.