Gordon Brown is preparing for a battle with the European Union over biofuels after one of the government's leading scientists warned they could exacerbate climate change rather than combat it.

In an outspoken attack on a policy which comes into force next week, Professor Bob Watson, the chief scientific adviser at the Department for Environment, Food and Rural Affairs, said it would be wrong to introduce compulsory quotas for the use of biofuels in petrol and diesel before their effects had been properly assessed.

"If one started to use biofuels ... and in reality that policy led to an increase in greenhouse gases rather than a decrease, that would obviously be insane," Watson said. "It would certainly be a perverse outcome."

Under the Renewable Transport Fuels Obligation, all petrol and diesel must contain 2.5% of biofuels from April 1. This is designed to ensure that Britain complies with a 2003 EU directive that 5.75% of petrol and diesel come from renewable sources by 2010.

But scientists have increasingly questioned the sustainability of biofuels, warning that by increasing deforestation the energy source may be contributing to global warming.

Watson's warning was echoed last night by Professor Sir David King, who recently retired as the government's chief scientific adviser. He said biofuel quotas should be put on hold until the results were known of a review which has been commissioned by ministers.

"What is absolutely desperately needed within government are people of integrity who will state what the science advice is under whatever political pressure or circumstances," he said.

The EU plans to raise the compulsory biofuel quota to 10% by 2020, but Brown is understood to be ready to challenge this plan. A senior government source said last night: "There is a growing feeling that we need to get all the facts. Some biofuels are OK but there are serious questions about others. More work needs to be done."

Sources say the government has no choice but to implement the guidelines next month because Britain is obliged under EU law to comply with the 2010 target.

But the report on biofuels, to come from the head of the Renewable Fuels Agency, Professor Ed Gallagher, may be used to challenge the more ambitious target for 2020, which is not set in law.

John Beddington, the government's current chief scientific adviser, has already expressed scepticism about biofuels. At a speech in Westminster this month he said demand for biofuels from the US had delivered a "major shock" to world agriculture, which was raising food prices globally. "There are real problems with the unsustainability of biofuels," he said, adding that cutting down rainforest to grow the crops was "profoundly stupid".

Britain will move cautiously in its battle with Brussels because José Manuel Barroso, the European commission president, is championing the 10% target for 2020. Barroso this month dismissed as "exaggerated" claims that biofuels can lead to increases in food prices and greenhouse gas emissions due to deforestation. But other members of the commission and other countries, including Germany, sympathise with Britain.

Brown was due to release a report touching on issues including biofuels, when he met Barroso in Brussels last month. But the prime minister decided that the time was "not right or ripe".

The prime minister made clear that Britain is wary of the target when he said last November: "I take extremely seriously concerns about the impact of biofuels on deforestation, precious habitats and on food security, and the UK is working to ensure a European sustainability standard is introduced as soon as possible, and we will not support an increase in biofuels over current target levels until an effective standard is in place."