CCGs will handle hardware, network services, support services and training for practices.
Hereford GP Dr Chris Frith, chairman of the user group for IT supplier EMIS, said: 'Money will be top sliced to pay off contracts and there will not be enough to fund the innovation that primary care IT needs.
'There has been a lull in innovations for primary care IT since the time prior to the 2004 GP contract.'
Dr Frith said current IT systems could cope with the Health Act's aim of integrating health and social care. But he warned that successful integration would depend on how those systems were used and on the quality of the data.
The DH has reported a £1bn saving from renegotiating its contract for the Lorenzo hospital computer system, which it hopes will boost use of electronic patient records. But the saving will not be used for IT.
The DH said the money would be used for patient care and frontline services.
Plans for CCGs to control primary care IT were revealed last month by the NHS Commissioning Board (NCB).
A statement from the NCB said: 'Work is still ongoing with PCTs to determine the level of current spend on GP IT, after which decisions will be taken to agree the allocation of funds to CCGs in 2013/14.'