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GPs who want to keep using EMIS will have pay for the system out of their own pocket, health minister John Hutton has revealed.
In a letter to a London GP, Mr Hutton said the Government will only give IT funding to PCTs for systems 'endorsed' by local service providers (LSPs) to the National Programme for IT.
'If GPs choose to run with systems that are not endorsed by their LSP, they will forfeit funding for the system unless the PCT chooses to support non-LSP solutions from their own resources,' he wrote.
Mr Hutton added that GPs who did not wish to change to the 'preferred solution' of the LSP would only be supported in the 'short-term'.
EMIS, which covers 56 per cent of GPs, has not yet signed a contract with any of the three local service providers.
With constraints on budgets growing tighter, PCTs are highly unlikely to fund IT systems they have not been given specific funding for.
The cost of maintenance and upgrades on existing systems would be up to £5,000 a year for an average three-partner practice, with a new system costing closer to £10,000.
Mr Hutton also stated that individual GPs who wanted to keep their system would have to give way if the consensus of the local health community was to use the same software across the entire area.
Dr Rob Hughes, the recipient of the letter, said he was disappointed that the department had a clear grasp of GPs' concerns about IT but could offer them no assurance that they were being addressed.
Dr Hughes, a GP in Greenwich, south London, and chair of the London GP forum, said: 'It's confirmation of the stupidity of the advisers to the minister.
'We should be past the old hard-line communist view that everyone must have a Skoda but the current strategy is in danger of giving every GP the same crap car they don't want to drive.'
Dr Paul Cundy, chair of the GPC's IT sub-committee, said Mr Hutton was ignoring the GP contract guarantee that choice of IT system is maintained and funded as long as the system is 'accredited' to the national programme.
He said: 'The agreement is systems will be funded provided they are spine compliant. Whether they are funded by LSPs or PCTs is not an issue for GPs.'
By Ian Cameron