Slovak officials have been sharply critical of Brussels' ruling, saying it was not generous enough to allow continued economic growth in one of the EU's poorer members, and that the process of setting its emissions cap was inappropriate. Brussels cut Slovakia's proposed carbon emissions cap by 25 percent.
"We want to protect Slovakia's economic interests, which means its economic growth, and to prevent an increase in the unemployment rate," Justice Minister Stefan Harabin said.
The country will seek at the European Court of Justice in Luxembourg to obtain a cancellation of the EU executive's decision on the quota, handed down on Nov. 29.
The European carbon market limits emissions of heat-trapping carbon dioxide (CO2) from heavy industry and is the 27-nation bloc's main tool to steer it towards its targets under the Kyoto Protocol on global warming.
The market is supposed to give industry too few permits to emit CO2 but in its first phase from 2005-07 businesses got more than they needed, crashing carbon prices and stiffening Brussels' resolve to be tougher next time around.
Slovakia may have trouble pursuing its challenge given the importance the European Union has attached to combating climate change, claiming global leadership on the issue last month.
"Clearly if they're successful it matters because everyone else will start doing it, which will count against (its chances)," said Merrill Lynch's Chris Leeds.
So far the Commission has demanded further cuts in 11 of the 13 phase two plans it has ruled on, only approving the emission caps proposed by Britain and Slovenia.
The Slovak government originally requested an annual limit of 41.3 million tonnes of carbon dioxide, saying that it deserved some extra leeway partly because it had closed nuclear capacity as part of the process of joining the bloc.
Harabin added the government has asked for so-called summary proceedings at the court, a fast-track process.
Slovakia says the emissions cut demand is unfair as it needs new electricity production capacity after it complied with another EU demand, to shut down one bloc at the older of its two nuclear power stations.
(Additional reporting by Gerard Wynn in London)