The government has commissioned an inquiry into the management of senior staff working in universities and the National Health Service following the Alder Hey body parts scandal.
The inquiry will be headed by Sir Brian Follett, who is retiring as vice-chancellor of Warwick University. It will look at appraisal and disciplinary procedures in particular and will report by the end of the year.
Michael Powell, executive officer of the Council of Heads of Medical Schools, said: "There has been a need to clarify the relationship between the two contracts used to employ clinical academics for some time."
Universities UK is to publish a report on the relationship between universities and the NHS.
A UUK spokesman said: "The review is an opportunity to clarify arrangements for staff who teach, undertake research and provide clinical services. Universities are committed to working in partnership with the NHS to manage these interlinked activities effectively to the benefit of all parties."
Clinical academics undertake research and provide clinical practice under an honorary NHS contract. They are paid for by a university endowment, the funding councils or by the NHS.
Tom Smith, a Nuffield Trust research associate based at the Judge Institute of Management Studies at Cambridge University, said: "The current arrangements between universities and the NHS are amateurish and in need of major reform."
A forthcoming report by the trust promotes university/clinical partnerships as a new framework for NHS/university relations. Last April, the trust published University Clinical Partnership: Harnessing Clinical Academic Resources that argued that the mission of quality service provision, research and teaching required better partnerships between the universities and trusts.
Mr Smith said: "The Redfern report into Alder Hey presents a crisis of governance between NHS and university partners. In total Redfern identified 20 major management flaws."
Mr Smith said that clinical academic contracts such as the one held by Dick van Velzen, who was highly criticised in the report, varied across the country and often involved "informal pooling" of funds.
"Any inquiry into contracts needs to look at the whole tangled relationship of funding and teaching and research strategies," he added.