The £105 million investment was part of the package that GPs voted for as ministers threatened to impose revisions to the contract earlier this year.
But LMC leaders say the money has either disappeared into PCT budgets completely or has come too late in the financial year to have an impact.
Nearly half of the £105 promised (£50 million) is earmarked for improving local enhanced services (LESs).
But the situation across PCTs is confused. A spokeswoman for Sandwell PCT admitted: 'We don't have any additional funding from the DoH. We are using existing money to invest in LESs.'
Of more than 40 PCTs contacted by GP, only Lincolnshire PCT could explain how it planned to invest in LESs.
Wessex LMC chief executive Dr Nigel Watson said the new clinical DESs, also worth £50 million, came too late in the year and the £50 million for local services was being swallowed into PCT budgets.
'It's a major issue that we went for option A (during the contract talks) to get a 1.5 per cent uplift. But we won't get any of the money for local services this year.'
Devon LMC chairman Dr Peter Joliffe told LMC members this week that the investment was spread so thinly that 'it hardly makes you think the DoH really wants this work done'.
Dr Chris Locke, chairman of Nottingham LMC, added: 'It is unfortunate. I'm not sure how confident we were that the 1.5 per cent would find its way into GPs' accounts in the first place.
Medical accountant Bob Senior described the DoH distribution of the 1.5 per cent as 'smoke and mirrors'. 'I would be very surprised if we see that 1.5 per cent making its way into practices this year,' he said.
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