European policymakers have been urged to reform the "exhausted" top-down funding mechanisms that force researchers into collaborations.
Enric Banda, president of Euroscience, which works to advance science and technology across Europe, told the SciTech Europe conference in Brussels last week that collaboration worked best when researchers determined their own projects and chose their partners as appropriate.
Most European research funding requires applicants to bid in multigroup and multicountry consortia. But Professor Banda objected to proposals that "force you to invent what you will do to get the money".
"The European Commission has done a great job but its mechanisms of collaboration are exhausted and it should find better ones," he said.
He also urged the scientific community to be "vigilant and united" against a trend towards science policy being determined "in offices by people who know next to nothing about science".
His message was echoed by Maria Leptin, director of the European Molecular Biology Organisation and a member of the management committee of the Initiative for Science in Europe, a network of European scientific organisations that was one of the original advocates for the creation of the European Research Council.
She described the ERC, which was launched in 2007 to fund individuals doing basic science, as the sole successful European funding mechanism.
The European Commission needed to develop "bottom-up" schemes that responded much more quickly to new potential research avenues, she argued.
"We can't wait until policymakers decide in two years that there may be a project to fund [in a particular area]," she said. "By then the motivation to pursue it will have gone."
Anthony Ryan, pro vice-chancellor for science at the University of Sheffield, said European-funded networks of excellence could, in reality, be "networks of mediocrity".
"My worry is that scientists are working hard to get money from organisations further and further away from research," he said.
The claims came as the Commission prepared to release details of its proposed €80 billion (£68.5 billion) spending plan for research and innovation between 2014 and 2020, known as Horizon 2020. This will be an increase of more than 45 per cent on the €55 billion budget for the current Framework Programme.
A spokesman for the Commission was unable to give details ahead of the 30 November release date, but said that funding schemes would be less programmatic and more based around societal challenges.
He also confirmed that the ERC's budget would be increased and said that accounting mechanisms would be made less onerous.
However, Professor Banda said the Commission had been promising simplification "for the past 30 years - but we haven't got very far".
Delegates also expressed anxiety about the Commission's increased focus on innovation. Several pointed out that universities' role in innovation was as much about bringing people together and nurturing creative and entrepreneurial thinkers as it was about increasing technology transfer.
Professor Leptin claimed that the former Communist bloc's policy of concentrating its research funding on applying the basic science conducted elsewhere had led to "not very much" of value.