Only a few years ago, European policymakers were hailing biofuels, made from plant matter such as corn, rapeseed and grasses, as the practical green alternative to fossil fuels, citing it as so clean that cars, vans and trucks might as well have been running on water.

But with the growing acceptance that producing many of these biofuels creates substantial carbon emissions from crop cultivations, those days are over.

Mathematical calculations being pored over by the European Commission could further cloud the reputation of biofuels as acceptably green, leading to a reduction in subsidies and tax breaks available under the EC’s renewable-energy directive.

The 2009 law came into force in December and imposes compulsory targets for the European Union’s 27-member states. At least 20% of their energy consumption must come from renewable sources by 2020, while 10% of their transport sector’s energy usage must be derived from renewable fuels under the ruling.

The Commission wants to be able to measure which biofuels are sufficiently green to count towards these compulsory targets and, therefore, qualify for lower duty and higher manufacturing subsidies.

EC officials have worked out a mathematical model by considering emissions as the biofuels are manufactured, consumed and released into the atmosphere when feedstock fields replace the natural environment.

That is complex enough, but now officials are embarking on a tougher task of modeling the additional CO2 caused by indirect changes in land-use wrought by biofuels production.

For example, the amount of emissions created when a wheat field is sown with rapeseed for biofuels production, forcing farmers to clear the nearby woodland to create a new field to grow their crops.

“The potential effects of indirect land use need to be properly weighed in our biofuels policy,” says EU Energy Commissioner Günther Oettinger. “It is in our interest to investigate this seriously to ensure we have legislation that avoids negative side effects.”

EC officials will report by July whether such land-use changes and associated emissions are sufficiently quantifiable to amend Europe’s renewable-fuels legislation. If the answer is “yes,” this could be bad news for auto makers that have invested in making flex-fuel vehicles.

Renault spokesman Mike Gale says vehicle manufacturers started to move away from biofuels three years ago, when incentives began to fade. The French auto maker is a case in point, with its aggressive electric-vehicles program.

That said, car companies continue to invest in the development of second-generation biofuels that use waste products as feedstock, although Sigrid de Vries, communications director for the European auto makers’ group, the ACEA, acknowledges second-generation technology has “a long path in research and development.”

Susan M. Cischke, Ford group vice president-sustainability, environment and safety engineering, is quoted as saying: “To unlock the full potential of biofuels, more investment into the development and implementation of second-generation biofuels is needed.

“Second generation biofuels that avoid the transfer of CO2 emissions into other sectors or regions are fully sustainable and should be encouraged.”

Although biofuels still are valued by the transport sector, their use in the EU last year fell below the 5.75% consumption target set in 2003 to an estimated 4.05%.

Nonetheless, in 2009, 12 million tons of oil equivalent (TOE), a unit of energy, was used by the EU transport sector, with Germany and France the largest consumers.

That was up from 10.2 million TOE in 2008, says renewable-energy monitor EurObserv’ER, which measures the annual progress made by renewable energies in each sector of each EU member state.

The European Biodiesel Board says the EU had capacity to produce about 24 million tons (22 million) of biodiesel, alone, last year.

The EC’s math modelers continue to wrestle with all of the complex data. Last summer, they released guidelines for the calculation of land carbon stocks on direct land-use changes.

Accordingly, a biofuels sustainability calculation measuring carbon content of virgin land (pre-biofuels production) must be based on areas roughly uniform before the feedstock growers came along.

It should have similar “biophysical conditions in terms of climate and soil type; management history in terms of tillage; and input history in terms of carbon input to soil,” the guidelines say. In other words, calculations must compare lands that have similar soils and similar plants, whether natural or farmed, before the feedstock growers.

The indirect land-use calculations, if officials can frame a model, likely will be even more complicated.