The research assessment exercise is discouraging entrepreneurship among academics, according to a report on chemical science spin-offs by the Royal Society of Chemistry.
But the Higher Education Funding Council for England has hit back, insisting that the RAE is inclusive of commercial research activities and does not discourage entrepreneurship.
The RSC report says: "Within universities, a mismatch exists between academic and commercial cultures. Universities by their very nature reward academics for their research and teaching efforts and do not generally encourage or reward entrepreneurship.
"This weakness is compounded by the research assessment exercise, which favours academic publication over commercialisation of research and therefore ties funding in a way that does not reflect overall government objectives."
Rama Thirunamachandran, director of research and knowledge transfer at Hefce, denied that there was any culture clash.
"You only have to look at the Higher Education Business and Community Interaction Survey to see that there has been considerable growth in all forms of third-stream research - patents, licences, consultancy and spin-outs. That comment is out of date."
He said the new RAE panels would have extensive guidance to ensure that all types of research output were assessed properly. Some panels, such as engineering, would have significant membership from businesses such as Rolls-Royce, Pfizer and GlaxoSmithKline and the public sector.
For example, a quarter of panellists for mechanical engineering will come from such user groups.
"The RAE is about assessing research of all types, including applied research and practice-based research. It is not assessing knowledge transfer," he said.
"Things such as patents can be submitted if they show the significance of the research being done. But the third stream is funded through the Higher Education Innovation Fund."
Sean McWhinnie, RSC manager of science policy, said that although the RAE does look at industrial research data, it does not take into account setting up spin-offs.
"I haven't seen anything in the RAE to explicitly measure entrepreneurship.
All metrics will be aimed at measuring research quality.
"If the Government wants this kind of thing, mechanisms must be put in place," he added.
Although there is now permanent funding for third-stream activities in the form of Heif, Dr McWhinnie said it was unclear whether its policy objective was to reward excellence or to encourage new institutions to engage in such activities.
"If the only game in town is the RAE, then it should take into account entrepreneurship," he said.
The report called for the RAEto be restructured to better recognise the balance between academic research and entrepreneurship.
The report also calls for university technology transfer offices to be run on a more commercial basis.
It said there was a shortage of "wet chemistry" laboratory facilities in science parks, which meant spin-offs were taking longer to move out of university laboratories.
As a result, companies had difficulty attracting funding because they were not yet seen as credible businesses.