The lawsuit, lodged with the EU's General Court, the bloc's second highest court, alleges several violations of European laws on transparency and democracy.
The suit was filed on 8 March by ClientEarth, Transport & Environment, the European Environmental Bureau and BirdLife International.
"That the Commission should choose to deny our rights on such a critical issue as the science underpinning our climate policies is astounding," said Tim Grabiel, staff attorney at ClientEarth.
At stake is the EU's commitment to its goal of getting a tenth of its road fuels from renewable sources such as biofuels by 2020 - a target that has spawned an EU industry worth around five billion euros ($6.8 billion) a year and a big market for imports from Brazil, Indonesia and Malaysia.
The four groups first sought access to the documents on 15 October 2009, and said the European Commission missed a legal deadline to release them under freedom of information laws on 9 February. Some reports have been released, but not all.
A similar request by Reuters has led to the release of 118 reports and e-mails, which reveal worries within the Commission that the EU set its 10% goal before fully assessing the impact of biofuel targets.
Making matters worse
Some of the documents raise the prospect of higher EU farm incomes, but cite concerns that plant-based biofuels could create food shortages for the world's poorest.
Others suggest biofuels can drive up demand for land, encouraging farmers in tropical areas to expand cropland into sensitive areas such as wetlands and rainforests - which would have a detrimental environmental impact.
Burning forests can release so much CO2 as to cancel out any benefits sought from the biofuels.
One leaked email says that taking account of biofuels' full carbon footprint could "kill" their role in the EU.
"Current EU biofuels policy guarantees that Europe will use lots of biofuels, but it doesn't guarantee reductions in greenhouse gas emissions - in fact it seems likely it will make things worse," said Nusa Urbancic of transport campaign group T&E.
"The first step to fixing this broken policy must be full transparency about what the true impacts are," she said.
The Commission was not immediately available to comment, but has previously said it is working very seriously to understand the indirect impacts of biofuels.
The case is not the Commission's only wrangle with environment groups over access to environmental documents.
The EU's own watchdog, Ombudsman P. Nikiforos Diamandouros, recently criticised the Commission for not releasing three letters that German car company Porsche had sent to former industry commissioner Guenther Verheugen.
The case originated with a complaint from Friends of the Earth Europe, which was trying to get hold of the documents as part of the debate over legislation to curb carbon emissions from cars.
(EurActiv with Reuters.)