The findings come as health secretary Andrew Lansley revealed that while some rules about consortia will be written into the Health Bill, others will be dictated by the NHS Commissioning Board.
The 2011/12 operating framework said consortia should be offered £2 per patient to cover their development and the cost of clinical backfill and training.
But a number of PCTs are failing to offer the full amount in cash, instead offering part of the fee in the form of PCT management support.
Even consortia that had received the £2 per patient funding warned that it was 'wholly inadequate' and failed to cover the time they spent on commissioning activity.
Dr James Kingsland, national clinical commissioning network lead in England, said development funding was meant to be paid in cash. He said: 'It is not just for consortia clinical leads' time, it is also for other professionals to look at data and begin to redesign services. It is meant to pay for that - it's not for PCTs to say they'll pay part in cash and some in managers' time.'
Northumberland LMC secretary Dr Jane Lothian said local commissioning pathfinders were receiving the development funding in cash, but raised concerns that 'it doesn't go very far'. She said: 'We are concerned about how to get engagement from practices in commissioning unless they are properly resourced.'
Dr Simon Brown, GP lead of Hunts Health consortium in Cambridgeshire said GPs were working double the hours on consortia activity that they were funded for. 'We think we have got shortfall in terms of ability to support the current consortia board,' he said. 'The £2 is wholly inadequate.'
Wessex LMCs chief executive Dr Nigel Watson said some PCTs in the area were giving pathfinders £1 in cash and £1 in PCT resource. 'PCTs don't have £2 per head sitting in their bank account to give us in cash,' he said. However, he added: 'I wouldn't say GPs are happy, but I would say there is a reasonable compromise in most areas.'
NHS Hampshire said the decision to offer a mix of funding and resource had been taken because local GPs want access to PCT support as well as resources for clinical backfill and training.
Derbyshire LMC secretary Dr John Grenville also said the PCT cluster in his area had held negotiations and agreed with consortia to provide part of the £2 development fee as a resource.
'The PCT will be appointing a chief operating officer and a deputy chief operating officer for each of the consortia,' he said.
Editor's blog: PCTs must pay consortia £2 per patient development funding