The guidance fails to address that practice-based commissioning is not being prioritised because PCTs are preoccupied with reconfiguration, GPC chairman Hamish Meldrum said.
Practices are also reluctant to take up practice based-commissioning because they are concerned about the impact of reconfiguration and how it will affect PCT deficits.
'Practices want to know what will happen if they merge with a PCT that is in deficit,' he said.
'My PCT is in deficit to the tune of £11 million. Colleagues in the neighbouring PCT are worried that if the two PCTs merge, the first call on practice-based commissioning savings will be to solve the neighbouring PCT's debts.
'The guidance is not clear about what happens to savings when a PCT is in deficit.Nor does it set a ceiling on the amount that PCTs can take for contingencies at the budget setting stage.'
However, NHS Alliance chairman Dr Michael Dixon believes the DoH's guidance has clarified some of the issues.
'The budget depends on last year's workload at next year's prices. PCTs can't deduct any deficits,' he said. 'The only loophole is that in extreme circumstances PCTs could draw on the savings. If we end up with PCTs raiding it there will be an outcry.'