Concern has been raised about the extent of pharmaceutical companies' influence in publicly funded research after a "precedent-setting" deal.
The alarm was caused by a call issued by the Engineering and Physical Sciences Research Council (EPSRC) in conjunction with the drugs giant GlaxoSmithKline (GSK).
It focuses on the "Synthesis of novel compounds for the potential treatment of respiratory diseases (drug discovery)", with the funders offering up to £1 million each.
Steven Allin, professor of organic chemistry at Keele University, said the collaboration marked a significant departure from previous EPSRC calls that were funded with private-sector partners and had worrying implications for academic freedom.
As the sole industrial partner, GSK would, Professor Allin said, have a major role in selecting what to fund, and it could choose to put commercial imperatives before academic considerations.
In addition, he argued that the call was so prescriptive that it amounted to little more than internal research for GSK, achieved at half the cost to the company.
He said: "GSK has recently announced serious job cuts in the UK, and now we see this company wishing to fund academics to provide ideas and carry out proprietary research work for them, at the cost of other EPSRC programmes."
Professor Allin acknowledged that co-funding with industrial partners was not unusual, but he said this call risked setting a precedent that would rope the research council in to similar deals to carry out "contract" or "service" work for private firms in the future.
He compared it unfavourably with another recent scheme, in which the EPSRC co-funded PhD places within synthetic chemistry with a number of pharmaceutical companies.
"In that particular call, the science to be studied was entirely down to the academic, and it was clear that, although the industrial partners might have a steer on what they felt was more interesting science, we still had academic freedom," he said.
The more recent call, which was issued last month, states that "applicants and their research organisations must be prepared to work on a research-collaboration agreement (incorporating intellectual property) with GSK".
Professor Allin said: "Where will the intellectual property go? There is no suggestion in the call that the IP will reside anywhere except with GSK, and therefore GSK shareholders will benefit, not UK plc. I feel quite strongly about that."
The EPSRC insists in a statement that the call is not a departure from previous collaborations and that it will include a full-peer review process.
"The call is an example of the EPSRC funding excellent-quality research with a clear exploitation route.
"To secure future funding from the Government, the EPSRC needs to demonstrate that the research it is supporting is not only of excellent quality but also has impact.
"Therefore, it is important to be supporting activities such as this alongside research supported through our researcher-led mechanisms," it says.
The intellectual property position "will depend on what is agreed between GSK and the applicant's organisation", the research council adds.