Professor Robert Watson called for the initiative – designed to cut greenhouse gas emissions – to be postponed while the impact of biofuels is reviewed.

He was joined by environmental and planning organisations which signed an open letter to Transport Secretary Ruth Kelly.

From next month, biofuels are to be used to partially power every vehicle in the country.

Under the Renewable Transport Fuels Obligation (RTFO), they will have to comprise at least 2.5 per cent of fuel at the pumps.

But Prof Watson cautions there are still doubts about biofuels.

The Department for the Environment's chief scientist said: "Many people still believe that some biofuels are indeed still sustainable from an environmental standpoint. I think we need to check that.

"It would obviously be totally insane if we had a policy to try and reduce greenhouse gas emissions through the use of biofuels that's actually leading to an increase in the greenhouse gases from biofuels."

Biofuels, mainly ethanol and diesel made from plants, have been promoted as an alternative to the use of liquid fuels in transport which account for about a quarter of global greenhouse emissions.

Asked about the start date for the RTFO, Prof Watson added: "I would suggest that we would indeed wait until the review is completed."

His comments came as groups including Oxfam, Royal Society for the Protection of Birds, Friends of the Earth and Greenpeace wrote to Ms Kelly saying "there is a very real risk that the RTFO will make climate change worse, not better".

Doug Parr, chief scientific adviser of Greenpeace, said: "From next month British motorists will be forced to pump biofuels into their tanks with no way of knowing if the so-called green fuels they're using are actually worse for the climate than regular fossil fuels."

Abigail Bunker, agriculture policy officer of the RSPB, said: "Biofuels threaten untold damage to unique wildlife habitats across the world.

"Their production is already causing the destruction of rainforest, peatlands and grasslands and the release of huge amounts of carbon stored by trees and soil.

"Thousands of people last week urged the Government to shelve its plans to force us to buy more biofuel. Ministers must heed those pleas not bulldoze through more biofuel use."

Kenneth Richter, biofuels campaigner at Friends of the Earth, said it would be irresponsible to proceed with the policy when experts were still "scratching their heads".

A Department for Transport spokesman said the RTFO would encourage the use of sustainable biofuels.

"Biofuels have the potential to help reduce the impact of transport on the environment but we have always been clear about the need to ensure that they are sustainable," the spokesman said. "The RTFO has at its heart a detailed sustainability reporting mechanism – going further than any other country – which will create a strong incentive for transport fuel suppliers to source sustainable biofuels.

"In addition, we recently announced a study into the wider impacts of biofuel production to help inform the development of both the UK and EU's policies in this area."