That means biofuels could produce more carbon emissions than gasoline over a 20-year time frame.
The impact assessment emerged as climate campaigners sued the European Commission on Monday for withholding a different tranche of data on the negative consequences of fuels from crops such as maize, wheat and palm oil.
"Our efforts to understand and influence EU biofuel policy have been repeatedly hampered by attempts to restrict access to documents," activist lawyer Tim Grabiel of ClientEarth said as he launched the court action.
"The Commission is running an opaque operation," he said.
The Commission's Joint Research Centre (JRC) said somewhere between 201 million tonnes and 1.092 billion tonnes of greenhouse gases would be released into the atmosphere due to the complex impact of "indirect land use change" from biofuels.
Those estimates were based on a scenario in which Europe's traffic burns no more than 7% of biofuels in diesel and gasoline by 2020.
But new strategy reports from the majority of the European Union's member states show they are actually intending to burn somewhere between 9 and 11% biofuels, implying that the real side-effects could be as high as 1.5 billion tonnes of carbon dioxide.
A Commission spokeswoman said seven of the 27 national plans were still missing, so an accurate assessment remains impossible. EU targets have been set for renewable energy in transport, but not specifically for biofuels, she added.
This year's fractious quest to understand the impact of EU biofuels policy has already led to allegations of bias, court action against the Commission and warnings that the probes will kill the nascent industry.
EU sources said Commission energy officials had fought to withhold the new work by the JRC for weeks, but relented on Friday.
In terms of land area, the new JRC study models a negative impact of between 8,209 square km and 52,372 square km due to indirect land-use change - in other words, an area somewhere between the size of Puerto Rico and that of Denmark.
The spare land would most likely be found in Brazil, Argentina and Asia, it concludes.
Freedom of information
In essence, the concept of "indirect land-use change" says that if you take a field of grain and switch the crop to biofuel, somebody, somewhere, will go hungry unless those missing tonnes of wheat are grown elsewhere.
The grain to make up the shortfall could come from anywhere, and economics often dictate that will be in tropical zones, encouraging farmers to hack out new land from fertile forests.
Burning forests to clear that land can pump vast quantities of climate-warming emissions into the atmosphere, enough to cancel out any of the benefits the biofuels were meant to bring.
But the whole picture is far more complex.
The EU biofuels industry counters that shortfalls in grain can be avoided in several ways, including by improving farming yields and cultivating abandoned land in Europe and Africa.
Furthermore, so-called "second generation biofuels" from waste straw and forestry offcuts are nearing commercialisation and have undisputed climate benefits.
To get a balanced picture of biofuels' impact on the environment, studies need to take account of the basic principle of using biofuels in the first place - the theory that fuel crops absorb as much carbon growing as they release when burned.
Any one-off impact caused by clearing forest or scrubland to increase farmland will be paid back over time as carbon savings due to biofuels add up.
The Commission research centre has attempted to pull together all the factors, however, and has found that over 20 years the European biofuels policy might actually lead to an increase in emissions - by 21% compared to gasoline, based on data from the executive's own agro-economic experts.
Another scenario paints a vision of 36% emissions savings on average compared to gasoline over 20 years, this time using figures generated by the International Food Policy Research Institute (IFPRI) in Washington.
Meanwhile, on Monday activist lawyers ClientEarth launched two court cases at the EU General Court against two powerful EU bodies - the European Council and the European Commission.
The first seeks greater transparency in the Council's review of EU transparency laws and the second seeks to unearth a hidden draft impact assessment on biofuels by IFPRI, which sources say was tweaked by the Commission in later drafts to improve the fuels' credentials.
"Citizens are being denied the right to participate in decisions that affect flagship climate policies and will not only affect their lives but those of future generations as well," said Grabiel of ClientEarth.
EurActiv with Reuters.)