Closing last month's NHS Confederation conference in Liverpool, NHS chief executive David Nicholson warned that both he and the Treasury were concerned about financial control.
PCTs had worked hard to achieve financial balance and this could be undermined if GP commissioning was rushed through, he said.
Mr Nicholson said even the most advanced practice-based commissioning groups were not ready yet and government policy would take longer than hoped to implement.
Other delegates expressed concern over how the NHS would ensure value for money as up to £80 billion a year in NHS cash is handed over to groups of GPs.
With growth in the NHS budget expected to fall in the next five years, King's Fund chief executive Anna Dixon said the policy was 'formed in a different era', and suggested the Treasury would delay the plans 'while it works out if this is a plan for today'.
NHS Confederation acting chief executive Nigel Edwards said the government's vision had 'potential', but expressed concern about the transition between the current system and GP-led commissioning.
'We could see a situation where GPs do not step up to this and hand over their commissioning to the private sector, and they become the new bureaucrats,' he told delegates.
Shadow health secretary Andy Burnham used Twitter to say the government's plans would 'turn the NHS from order to chaos'. The Treasury was 'right to block' the plans, he said.
Mr Edwards called for a new GP contract that incentivises the commissioning role as well as encouraging practices to federate.
He said any new contract must be 'cost-neutral', meaning extra money spent on setting up commissioning is balanced by savings elsewhere.
Mr Edwards called for GP consortia to be given budgets by local authorities to provide health and social care together.