Full details of how the contract will work were published last week in amendments to the GMS statement of financial entitlements.
Practices will be able to choose three areas of prescribing on which their QOF targets will focus, and to negotiate different achievement thresholds.
The 2011/12 GP contract, which took effect from 1 April, puts 10 per cent of QOF pay into a new quality and productivity domain. Under the deal, practices will internally review prescribing behaviour and compare themselves against a local group of practices.
They will then agree targets to improve prescribing with this group and the primary care organisation. Practices will also create care pathways to avoid inappropriate referrals and emergency admissions.
Dr Deborah Colvin, chairwoman of City and Hackney LMC in London, said although the principle was sound, she was 'anxious' about its execution.
Without careful audit, the system could produce postcode lotteries across prescribing, referrals and emergency admissions. 'This may make care less equitable,' she said.
She added GPs must ensure targets were created 'fairly and honestly' to avoid accusations of abusing the system.
Dr Colvin criticised the publication of details of the contract after the start of the financial year. 'Getting set up and organised will take a long time,' she warned.
Dr Jane Lothian, secretary of Northumberland LMC, agreed: 'This will not be straightforward. There will be quite a bit of work involved.'
Dr Lothian welcomed the contract changes overall, and said the prescribing indicators mirror 'very useful' work already underway in her area.
But locally determined, sophisticated targets could be blocked by a lack of equivalent national data against which to judge performance, she said.
Dr David Jenner, GMS/PMS lead at the NHS Alliance, said: 'Local process markers are fine but I would be very anxious about localising outcome targets in QOF - after all, it's a national contract.'
He added: 'My guess is PCTs will withdraw prescribing incentive schemes as this is now here.'
GPC deputy chairman Dr Richard Vautrey said: 'I don't see this as a postcode lottery at all.' He said the new indicators would encourage doctors to work to come to a consensus about what works in primary care.