Biofuels such as biodiesel from soy beans can create up to four times more climate-warming emissions than standard diesel or petrol, according to an EU document released under freedom of information laws.
The European Union has set itself a goal of obtaining 10% of its road fuels from renewable sources, mostly biofuels, by the end of this decade, but it is now worrying about the unintended environmental impacts.
Four major studies are under way.
Chief among those fears is that biofuel production soaks up grain from global commodity markets, forcing up food prices and encouraging farmers to clear tropical forests in the quest for new land.
Burning forests releases vast quantities of carbon dioxide and often cancels out many of the climate benefits sought from biofuels.
Biodiesel from North American soybeans has an indirect carbon footprint of 339.9 kilograms of CO2 per gigajoule - four times higher than standard diesel - said the EU document, an annex that was controversially stripped from a report published in December.
Editing the report caused one of the consultancies, Fraunhofer of Germany, to disown it partly in a disclaimer.
But it has now been made public after Reuters used freedom of information laws to gain a copy.
The EU's executive European Commission said it had not doctored the report to hide the evidence, but only to allow deeper analysis before publishing.
"Given the divergence of views and the level of complexity of the issue [...] it was considered better to leave the contentious analysis out of the report," the Commission said in a statement. "The analysis prepared under this study applied a methodology which by many is not considered appropriate."
The annex adds some weight to a growing dossier suggesting biofuels are not as green as once thought -even the more advanced, second-generation biofuels made from wood chips.
"For the third time in six weeks the [European] Commission is forced to release studies about the climate effects of biofuels," said Nusa Urbancic of T&E, a campaign group for green transport.
"And for the third time these studies show that land use is the most important factor in deciding if biofuels make sense or not," Urbancic said.
Biodiesel from European rapeseed has an indirect carbon footprint of 150.3 kg of CO2 per gigajoule, while bioethanol from European sugar beet is calculated at 100.3 kg - both much higher than conventional diesel or gasoline at around 85 kg.
By contrast, imports of bioethanol from Latin American sugar cane and palm oil from Southeast Asia get a relatively clean bill of health from the study at 82.3 kg and 73.6 kg respectively.
But one of the scientists involved with the study cautioned that much work remained to be done before the issue was properly understood, and that no firm conclusions could be drawn about the relative merits of different biofuel sources.
"The major point is that we have to do more work, develop new sustainability criteria and we have to be very careful about the origins of biofuels," said Wolfgang Eichhammer of Fraunhofer.
"We must also find a way of excluding the inefficient biofuels," he added.
Eichhammer said he had made his stand with the disclaimer to protect the neutrality of science, and emphasised the value of ongoing Commission studies into the problem.
(EurActiv with Reuters.)