Dr Mike Bewick, medical director for NHS Cumbria, where GP commissioning is well-developed, predicted just 20 per cent of consortia would be ready to take over PCT functions fully by 2013.
'You have to develop relationships with managers and other health professionals.
That takes a long time and there is a lot of pain,' he said.
Dr Hugh Reeve, GP and chairman of Cumbria's Westmorland Primary Care Collaborative, said that if GPs were not already working closely with their PCT on commissioning they would not be ready by 2013. He suggested that where there was a poor relationship between GPs and the PCTs, the PCT should be abolished sooner to stop GPs' progress being hindered.
'If there is a lack of trust or a poor relationship between GPs and the PCTs, I say, get rid of the PCT now,' Dr Reeve said.
'If you haven't got the relationship we've had over the past two years, I struggle to see how you can hand over commissioning effectively.'
Dr Bewick and Dr Reeve were giving evidence to an inquiry into the NHS White Paper by the All Party Parliamentary Group on primary care (APPG) in London last week.
Dr Reeve said that while GPs in some areas had been commissioning jointly with their PCT for years, 'some are starting from a point they see as war with their PCT'.
He called for the DoH to clarify what will happen to GP consortia that overspend.
'The government has to decide whether it will allow these organisations to fail because I think a lot will. 'If you look to the US, many similar organisations did,' he said.
Health minister Lord Howe, also giving evidence to the APPG, said it was 'only a short step' to convert a practice-based commissioning consortium into a GP consortium, and the reforms were on track.