In a 'survival guide' for the 2013/14 GP contract, the GPC urged practices to carefully consider whether each new indicator should be targeted and to remember that QOF 'remains voluntary'.
It said that although NHS management had seen QOF achievement as a mark of practice competence, the huge demands of the new contract mean practices should take a 'more cautious and balanced approach'.
The GPC said: 'As practices start to take this approach, some will see a reduction in their QOF achievement. Far from indicating a struggling practice, a reduction in QOF achievement may be the result of business rationale and wholly appropriate clinical decisions.
'Practices need to consider all costs associated with the new work against the resources available.'
If practices followed the advice it would mark a shift towards QOF being a 'menu' of possible targets, in contrast with GPs feeling obliged to chase all available points as before.
GP leaders said it was 'inevitable' exception reporting will rise across many new areas of QOF, yet warned that practices may be forced to justify any increases as the DH does not expect a significant rise.
The GPC also repeated warnings that the contract changes will push up workload, reduce income, harm care and affect patient access to GP surgeries.
The GP contract was set by the government for 2013/14 following a breakdown in talks in autumn 2012. A consultation followed between December and February, and the final details were announced in March.
These included a raft of new targets proposed by NICE, some of which the GPC had rejected out of hand.