High-cost subjects such as chemistry, physics and chemical engineering will be hardest hit, according to the 1994 Group, receiving £1,246 a year less per student in 2012-13 than under the current regime. The calculation is made for a university charging tuition fees of £9,000 a year and does not take inflation into account.
The mission group warns that universities could be forced to cut places on such courses, as well as in languages and other strategically important and vulnerable subjects.
It voices "serious concerns" in its response to the Higher Education Funding Council for England's consultation on changes to teaching funding.
Under the proposals, nearly all state funding for teaching in the arts, humanities and social sciences will end. The lost income will have to be made up from higher fees.
While some teaching funding for science, technology, engineering and mathematics subjects will continue, the 1994 Group says the proposed levels will not cover costs.
It claims that the shortfall is partly caused by extra spending on schemes to attract and retain poorer students: universities intend to spend an average of 26 per cent of the additional fee income above £6,000 under the new funding regime on access measures.
These changes would result in a fall of £246 per band B student and £1,246 for higher-cost laboratory courses, despite the extra income from higher fees.
Paul Wellings, vice-chancellor of Lancaster University and chair of the 1994 Group, said lab-based courses would be disproportionately affected.
"Even universities charging the highest fees won't be able to cover the full costs of delivering these subjects," he said. "This may undermine the sustainability of the subjects, which have been identified as priority areas."
Cheaper humanities courses are likely to proliferate thanks to "unhelpful and inadvertent incentives", the 1994 Group adds.
Andy Westwood, chief executive of Guild HE, said many specialist subjects, including art, drama and farming, could also suffer.
"There is a significant bias against high-cost subjects and the ability to cross-subsidise them is also reduced," he said. "I think there is a danger of an overflow of cheaper subjects."
The 1994 Group submission also asks Hefce to reconsider the withdrawal of teaching funds for postgraduate study in classroom-based subjects, saying it will have "serious implications for the health of postgraduate education".
It goes on to voice "deep concerns" about plans to allow universities to compete to recruit as many students scoring AAB or higher at A level as they wish, warning that elite institutions may simply "replace" students removed from quotas with AAB students.
Submissions from other mission groups, including the University Alliance and Million+, concentrate on how the AAB system would combine with plans to remove 20,000 places from general quotas and auction them off to institutions charging £7,500 a year or less.
Million+ calls for the introduction of the market-creating mechanisms to be deferred until 2013-14.