Clinical audits often involve the collection of non-routine data, and knowledge of how this is collected and stored is often held by individual staff.
Robin Burgess, chief executive of the Healthcare Quality Improvement Partnership, a charity set up by groups including the RCGP to improve healthcare quality, said these staff could be lost during NHS reforms.
'We need to make sure that the knowledge in PCTs in not eroded by poor transfer,' he said.
GP consortia that fail to take this on board could miss out on improvements in efficiency that follow clinical audits and cost savings in areas such as prescribing budgets, he said.
Professor Ruth Chambers, a GP and practice-based commissioning clinical lead in Staffordshire, said clinical audit would be vital to GP commissioning.
'If we redesign services, we'll need clinical audit to check that patients experiencing different service provision have at least as good health outcomes as with the old service and we haven't sacrificed quality and safety to get costs down,' she said.
Stephen Ashmore, who managed the Leicestershire Primary Care Audit Group and now provides training through the Clinical Audit Support Centre, said the NHS had repeatedly lost clinical audit staff during reorganisations.
Consortia need to think ahead to avoid suffering the same fate, he said.