The Government was this week accused of breaking a pledge to increase funding to new universities under the "third-stream" scheme for improving academic-business links.
Indications ahead of Friday's allocations of the £187 million second round of the Higher Education Innovation Fund suggest that old universities will win the lion's share of awards.
Roger Brown, principal of Southampton Institute, said he had been promised that larger allocations would be made to non-research-intensive institutions to assist applied research projects.
Birmingham University, for example, has been given £6.2 million compared with £2 million last time, while Middlesex University asked for £2.4 million but got £1.2 million - only £700,000 more than the first round.
The deputy vice-chancellor of one new university in the North-west said there was "considerable disquiet" among colleagues.
Michael Driscoll, vice-chancellor of Middlesex and chairman of Campaigning for Mainstream Universities, said: "It's part of the general pattern of creating a small elite of well-funded universities at the expense of the mass of the higher education sector."
The fund is a partnership between the Department of Trade and Industry, the Higher Education Funding Council for England and the Department for Education and Skills.