A series of burdens on universities and colleges have been generated by weaknesses in the way the funding council fulfils its various roles, the report says.
The lack of a direct link between funding and outputs such as teaching quality have resulted in a growth in ad-hoc programmes geared to specific results.
Unsuccessful bids for funding cost institutions money. Even successful bids take months to come through, holding up other decision-making processes.
Hefce was praised for asking all higher education institutions to produce strategic plans. However, the study noted that short-termism and opportunism continue.
One vice-chancellor was quoted as saying: "The strategic plans submitted to Hefce are not the strategic plans of the institution. They are bidding documents to position ourselves in anticipation of when the inevitable 'special initiatives' come round."
Numerous overlapping audits and interventions result from the failure - blamed on Hefce - to ensure that internal assurance systems satisfy stakeholders. Similarly, data demands from stakeholders have led to a growth in duplicated, low-value data returns.