Concern about the proposed bonus for successful consortia is set out in NICE's response to the White Paper Liberating the NHS.
Where providers serve patients covered by more than one consortium, 'it may be difficult to determine whose commissioning is producing changes in a GP consortium's outcomes', the institute said.
NICE warned the premium needed careful planning and piloting and called for criteria to calculate how to share it among practices.
GPC deputy chairman Dr Richard Vautrey said: 'We would share concerns about this. Measuring any form of outcome is complex and needs to take many factors into account.'
Removing practice boundaries may further complicate efforts to track the causes of changes to outcomes, he said. This is because practices will be susceptible to social and economic factors from a wider geographical area.
NICE said more clarity is needed on the roles of consortia and the NHS Commissioning Board in managing practice performance.
It also expressed concerns about potential problems if populations covered by GP consortia do not match those of local