In an exclusive interview with GP, NHS Confederation chief executive Mike Farrar said clinical commissioning groups (CCGs) would face more difficult circumstances and tougher decisions than PCTs.
He said CCGs may struggle to find support from experienced PCT managers as many would already have left the NHS.
Mr Farrar said it was 'very important' that the NHS recognised just how big the challenge was for CCGs.
'The circumstances CCGs face are tougher, there are tougher decisions to take, and PCT managers tended to have a career in being developed as managers,' he said.
'PCTs also had slightly easier relationships with the organisations around them.'
Mr Farrar said that although GPs were 'very skilled individuals' they may lack some of the knowledge that is needed to run CCGs.
He said clinicians often had little experience in controversial decision-making, consulting the public and doing media work. 'Not every GP will be particularly happy giving lots of quotes to their local newspaper,' he said.
Mr Farrar said CCGs would need 'good quality and experienced people' to provide advice. 'We feel that there needs to be a huge amount of support available to them quickly. We need clarity about where they get that support, who they can employ and what resources will be available to them,' he said.
Mr Farrar warned that recent management cost targets had left management levels 'dangerously low' in some PCTs.
CCGs may struggle to recruit PCT managers previously made redundant and may be unable to employ their first choice of manager, he added.
Mr Farrar also said that CCGs might have to pool their £25-£35 per head management allowance in order to make ends meet. 'Does every CCG use all those resources locally, or do you share to support you on your commissioning work?'