Leading figures in British science are trying to wrestle the new European Research Council away from the European Commission's control.
The exact governance arrangements of the new European council, which will fund up to €12 billion (£8.15 billion) of basic research, remain up in the air.
The situation is fuelling fears that scientific decisions could be compromised by the political demands of the commission.
At a private meeting last week, UK research council chief executives urged Lord Sainsbury, the science minister, to fight for the ERC to have total independence from the commission in the medium term.
A senior research council insider said that the chief executives accepted that the ERC would be set up as an executive agency of the commission at first.
But he said they were determined to push for a so-called 171 agreement once it was up and running. This would mean that the council would not report primarily to the commission and would be an arm's-length body.
Such a strong line could prove difficult to enforce.
A high-level source at the European Parliament in Brussels said: "The parliament thinks the commission has been very secretive about all this.
There is a definite feeling that the ERC will inevitably become just an extension of the commission. I think there is no doubt who will be pulling the strings."
Another senior UK source said that Janez Potocnik, the European Commissioner for Science and Research, was assuring scientists that the council would be independent. But officials admitted privately that this was unrealistic. "The question is, are we prepared to trust the commission?" he asked.
Giles Chichester, chair of the European Parliament's research committee, said: "I would say there is a widespread sense of the council needing to be not just another commission-run agency, but how we achieve that is another problem."
Fotis Kafotos, chair of immunogenetics at Imperial College London and one of the 22 people appointed in July to run the new science council, said:
"We have to start now with an executive agency. If not, the whole project is in danger and we will lose momentum."
He added that at a meeting of the council in Brussels last week, Dr Potocnik had been very robust about the need for the ERC's scientific decisions to be independent of the commission.
But he said: "We don't know who the next commissioner for research will be.
People who are pushing for Article 171 certainly have this at the back of their minds and I think that is a reasonable concern."
The council agreed last week that the ERC must have a secretary-general, probably from the science community but with management experience, to link the executive agency and the council.