EC President Juncker and Commissioner Moedas met with a high level group of independent scientists who will now be responsible for coordinating national academies and other scientific bodies in providing advice to the commission.
The future mechanism aims to draw on the wide range of scientific expertise in Europe through a close relationship with national academies and other bodies.
Commissioner Moedas said: "In combination with the forthcoming proposals on better regulation, the new model for independent scientific advice will contribute to the Commission's continued pursuit of the best possible evidence-based policy.
"This will be a significant step forward for an effective European Commission that delivers for citizens, and addresses the major societal challenges which Europe faces."
In November 2014, Mr Juncker abolished the post of Chief Scientific Adviser to the EC, held by Professor Anne Glover, a move that the National Farmers' Union in Scotland (NFUS) described as a "backward step".
NFUS president Allan Bowie said: “Since Professor Glover’s post was abolished last year, the commission has already brought forward unhelpful legislation on re-nationalising the authorisation process of GM."
Mr Bowie added that his organisation believed that policy-making in Europe ought to be driven by science, and he was pleased to see the commission making progress on this issue.
He continued: “However, we will be continuing to ensure that this is a genuine effort to ensure that policy is free from politics. We would expect this body to be as robust as Professor Anne Glover was and stand up for science in the policy making that comes out of Europe.
“Science can provide us with enormous possibilities, particularly as Europe’s farmers attempt to meet the challenge of feeding a growing world population in volatile market conditions."