Manually compiling the data required for clinical commissioning groups (CCGs) to go live could cost the NHS £373m a year in management time, it is claimed.
For a CCG to be ready for full authorisation to go live in April 2013, it is required to be able to "prove clear and credible governance arrangements".
These include identifying financial controls and QIPP target plans.
It is argued that due to the "complexity locked in GP practices", manually compiling and analysing the data could cost the average GP practice more than £3,700 a month.
If a practice chooses to go down the manual route, Graham Poulter, Managing Director of iQ Medical, claims it will be "inevitable" it will end up choosing between compromising either the quality of the data, or the quality of care they provide within their budgets.
By automating the data collection process, Mr Poulter argues a CCG of 12 GP practices could save more than £420,000 in management time a year.
"The government's white paper, An Information Revolution, stressed the need for practices to begin 'recording data once and using it in many ways'," he said.
"Aiming for full authorisation by April 2013 is the perfect opportunity for CCGs and their member GP practices to do this: the data needs to be compiled somehow, so taking the time to automate the system now could help CCGs hit this target and save them hundreds of thousands of pounds a year in maintaining the data."