Oxford University is filing a complaint to the Office of Science and Technology over the research councils' handling of claims for research project costs.
The university says it has lost Pounds 3 million and is facing "considerable cutbacks" in library provision and pump-priming funds because the research councils are not sticking to the rules for payment of costs as they take over financial responsibility from the funding councils.
A report on Oxford's financial statements for 1993/94 estimates that of Pounds 11 million by which its funding council grant was reduced for the year, under the transfer of funds to the research councils, the university recovered Pounds 5.7 million in indirect costs and less than Pounds 3 million in direct costs.
It says increases in departmental deficits, now running at Pounds 6 million, are "in the main the result of departments finding it impossible to achieve the targets set for recovering additional direct costs from research councils".
John Peach, chairman of the university's general board, said the university had compiled a dossier on how the research councils had "failed to obey the rules".