Funding chiefs should demand more than £200 million extra for research to prevent universities losing out when they do charity-funded work, according to a report published this week.
The report by JM Consulting recommends that the Higher Education Funding Council for England "seek an increase in its research funds so that it can provide an explicit stream of additional infrastructure support to higher education institutions on their eligible charity-funded research".
The cost of supporting the indirect costs of charity-funded research has been a bone of contention for years.
Notwithstanding the millions invested in infrastructure by the Wellcome Trust, the world's largest medical research charity, charities argue that it is the government's job to provide the basic research infrastructure.
But universities do not receive government support for the infrastructure required for charity-funded research.
In 1999-2000, charities spent £484 million on university research. This was about 25 per cent of universities' research grant and contract income.
Research councils pay a 46 per cent overhead when awarding grants to universities. If charity overheads were to be met at the same level by the government, the funding council should be asking for an extra £220 million.
Mike Dexter, director of the Wellcome Trust, said: "We welcome this report, which acknowledges research charities' unique contribution and the importance of a partnership between government, charities and universities.
"This is the right way to maintain Britain's international scientific status and we are looking forward to working with others in addressing these issues."
JM Consulting proposes a tripartite approach in which the higher education sector, charities and the funding council work together to put charity-funded research on a secure long-term footing.
A tripartite approach "would be one of partnership of the higher education and charitable sectors working together to maximise the benefits from limited funds for research and investing to maintain the research base for the future".
A funding council spokesman said: "We look forward to a closer dialogue between the higher education sector and charities to take forward recommendations in the report."