"We are writing to seek assurance that the Commission is giving due consideration to science in its energy policy, after several instances in which the best available science was dismissed," the letter says.
In September 2009, Barroso made a speech calling for "a fundamental review of the way European institutions access and use scientific advice".
But the letter cites five world-class studies for the EU which, it says, all agree that the Indirect Land Use Change (ILUC) effects of biofuels "could not only negate the expected carbon savings, but even lead to an increase in emissions."
The most recent, a report by the scientific committee of the European Environment Agency (EEA) slammed the official EU policy that biofuels are 'carbon neutral' as a "serious accounting error" with "immense" potential consequences.
The 19 scientists on the panel decided that it neglected the fact that other carbon-absorbing plants would have grown on fertile land used by the biofuels, so any carbon absorption from the biofuels themselves was being "double-counted".
The letter's signatories include ActionAid, Birdlife, ClientEarth, European Environmental Bureau, Oxfam, Transport and Environment and Wetlands International.
"I can only rejoice that these seven NGO’s have done that [sent the letter]," Dr Pierre Laconte, the vice-chair of the EEA panel responsible for the report told EurActiv.
A spokesperson for Mr Barroso would only say that "the president has received the letter and there will be an answer in due time."
The missive was prompted by a statement from an EU spokesperson on September 14th that research by the acclaimed Princeton scholar Tim Searchinger which underpinned the EEA's report, "seems not to be an actual good contribution to the debate" and had been "rebutted by other institutions."
"We have used Tim Searchinger's work and we invited him to address us – as we did industry people," Dr Detlef Sprinz, the chairman of the EEA panel, told EurActiv. "I find his work rather important," he added. "It has been published in some of the best journals that we have."
The science involved in the report is of crucial importance. On Page 8, the EEA report cites the IEA as saying that biofuels could provide 20% of the world’s energy by 2050, and the UNFCCC claiming that bioenergy could supply 800 exajoules of energy per year (EJ/yr).
But today's entire global cultivatable land for food, feed, fibre and wood only has a chemical energy value of 230 (EJ/yr), just over a quarter of that figure.
The implication, says Dr Laconte, could be a complete collapse of the world's rural economies, as they are displaced by carbon-emitting feedstock-based biofuels.
"Agriculture could be wiped out and therefore the food it produces, leading to a problem of food scarcity," he said.
The problem was one of "decisions on biofuels that have been taken, which are not easy to change and which have huge consequences."
"People have praised a method of saving emissions which has proved not to be true," he said.
Since 2008, EU member states have been obliged to raise the share of biofuels in the transport energy mix to 10% by 2020.
But because this can count towards their separate target of a 20% share for renewables in the overall energy mix by 2020, the EU says that biofuels will ultimately account for 2.5% of overall energy, or an eighth of the total.
Environmentalists cite an EEA report to argue that the figure would be even higher if it counted, for example, the annual 4.4 million tonnes of bioliquids for heating that can make up member states' renewable targets. These can be provided by feedstock-based biofuels such as palm oil.
Asked by EurActiv whether the EU's 20% renewables target was legitimate and could be trusted, Tim Searchinger, the scientist at the heart of the row, replied: "No, absolutely not."
"The EU energy targets calls for a little bit more than half of all the targets to be met by bioenergy," he said. "You could do that by chopping down your forests and putting them in a [biomass] power plant, or turning the Amazon into a parking lot for wood pellets."
Forests in America were already being chopped down for such wood pellet fuel for the EU, according to Searchinger.
"It's wrong, and everybody knows it," he said. "Carbon accumulating forests absorb a third or more of the world's greenhouse gas emissions – on a gross basis. If you just get rid of that sink its doing as much to increase global warming as increasing your [fuel] source."