Politicians and scientists have called on the head of the EU to reinstate the position of chief scientist adviser to the organisation, a job currently held by a Scottish professor.
Supporters say Professor Anne Glover's post was vital to ensure EU policies on important issues like tackling Ebola were underpinned by evidence.
The decision to abolish the role is all the more controversial because it comes after concerted lobbying by groups opposed to genetically modified foods.
Ms Glover, a biologist and professor of molecular and cell biology at Aberdeen University, is also a former chief scientist for Scotland.
She has argued opposition to GM crops is "a form of madness".
Pamela Nash, the Airdrie and Shotts MP who sits on the Commons Science Committee, called the decision to scrap the role of Chief Scientific Adviser (CSA) 'outrageous', and urged EU Commission President Jean-Claude Juncker to reinstate it.
She said: "It is absolutely crucial that policy is informed by evidence. This is why my committee has long supported CSAs in every Whitehall Department. This decision will damage the ability of politicians to produce informed policy by effectively removing independent scientific advice from the European policy making process.
"At a time when we are facing huge challenges such as climate change, global population growth and the spread of diseases such as Ebola, this is a highly dangerous decision."
Ian Duncan, the Conservative MEP, also hit out at Mr Juncker, saying he had pledged to keep the role.
Mr Duncan said: "Anne Glover is a remarkable scientist who has dedicated herself to provision of rigorous scientific advice, facilitating credible policy decision making in the European Union.
"It is sad that Jean-Claude Juncker has broken his promise and caved to a small, politically motivated group."
Earlier this year Greenpeace and eight other campaign groups wrote to Mr Juncker urging him to abolish the position, arguing that it concentrated "too much influence in one person".
More than 20 scientific bodies, including the Royal Society of Chemistry, later wrote calling on him to ignore the demands.
The commission has denied the abolition of the post had anything to do with Ms Glover's views.
A spokeswoman said the post had "expired" and Mr Juncker had yet to decide "how to institutionalise" scientific advice.
But the decision was welcomed by those who had lobbied against her role.
Doug Parr, chief scientist at Greenpeace UK, said: "Scientific advice is the cornerstone of sound policy-making.
But the role of chief scientific adviser to the commission ended up hindering this process instead of helping it."
The National Farmers' Union warned the abolition of the post appeared to be a "backward step for science".
Leading scientists including Sir Paul Nurse, the president of the Royal Society, have also condemned the move.
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