Two-thirds of university and college staff feel the Higher Education Funding Council for England is bureaucratic and a third feel it is inflexible and lacks transparency.
The fourth Mori survey, conducted on behalf of the funding council to look at the relationship between the council and the sector found that the research assessment exercise had strained relations, largely because universities had not got the funding they expected.
Michael Driscoll, chair of the Coalition of Modern Universities, many of whose members lost out severely in the exercise, said: "The RAE has soured relations between the funding council and the sector."
Overall, however, 74 per cent of staff have a favourable view of Hefce, compared with 59 per cent three years ago. But there is confusion about Hefce's role - whether the council is meant to challenge government decisions or simply carry them out.
Sir Howard Newby, chief executive of Hefce, said: "The role of the Hefce is that of a buffer body between the government and higher education institutionsI We robustly represent the needs of higher education to government, and convey the views of government to higher education."
He said it was difficult for people to judge how effective Hefce was in advancing the interests of higher education because much of the its advice to government was in confidence.
As a result of the Mori report, the council is seeking to reduce administrative burdens and to improve awareness of how it works. It is also seeking to increase the visibility of the Hefce board and make better use of events at regional and national levels.
The Mori survey was conducted between December 2002 and January 2003 and encompassed the views of staff in 25 universities, 17 higher education colleges and 29 FE colleges from all nine English regions.