The post had been established under the previous European Commission president, José Manuel Barroso during his second term.
The European Commission and President Juncker are now considering how they will fill the void of scientific advice over issues such as technology, innovation and development.
The advisor’s role has been seen as being key to providing independent advice to the president.
The present European Chief Scientific Advisor, Scottish scientist Anne Glover took up the role in 2012 but when the new president and his team took over at the end of October and the advisor role came up for renewal, the president decided to scrap the position.
She will leave the post in February.
In the UK, the chief scientific advisor provides neutral, scientifically-sound advice particularly on emotive topics such as genetically-modified crops and nanotechnology.
The move by president Juncker has been greeted with a clamour of shock and outrage from some sections of the scientific and agricultural communities.
However, it could be that President Juncker has been persuaded to scrap the post because of a concerted campaign by a group of NGOs shortly before he took the reins as president to have to post abolished.
The groups included organisations such as the Pesticide Action Network, the Cancer Prevention and Education Society and Greenpeace and their concerns that the advisor was unaccountable were raised soon after Anne Glover had issued her appraisal of genetically modified crops.
The environmentalists were angry that she had said there was a scientific consensus that GM crops were safe.
The scientific and agricultural community have leapt in to support the role and are crying out for the position to be retained.
UK National Farmers’ Union President Meurig Raymond said: “We warmly welcomed the appointment of Professor Glover as we firmly believe that strong and independent science should be at the centre of policymaking in the EU.
“It is deeply troubling that the new European Commission has taken this decision. This appears to be a backward step for science. At a time when we need to address serious concerns around food security, energy security and the collective EU response to the threat of climate change; it is deeply concerning that the voice of science should be stifled.
“We would like to put on public record our sincere thanks to Professor Glover for her work. Professor Glover has championed the importance of science and innovation to drive growth in the EU. We now urgently seek assurances from the Commission as to how the role that she and her office played will be continued.”
Prof. Martin Barstow, the President of the Royal Astronomical Society, said: "It is widely accepted that investment in scientific research is an important element of economic growth and that political decisions should be firmly evidence-based. Therefore it is enormously disappointing and worrying that the role of Chief Scientific Advisor to the European Commission has been abolished.
“This suggests that the commission does not understand or value the role of independent scientific advice, with potentially grave implications for the future EU science programme - in Horizon 2020 and the European Research Council - and for EU policy in general. I strongly encourage the Commission to reconsider the decision and re-instate this position."
Mark Lynas, environmental campaigner and author said: “This is a dark day for science in Europe. Instead of having scientific advice at the heart of European policymaking, the Juncker Commission clearly wants to remove any person who might bring inconvenient scientific truths to the top EU table.
“Sadly, this is all too consistent with European moves to back away from evidence-based policymaking – if you can’t change the science you muzzle the scientists or keep them out of the room when powerful people are taking decisions.”
