DoH figures for May, released last week, showed that Somerset and Dorset, Kent and Medway, and Hampshire and the Isle of Wight SHAs had zero uptake of the first incentive payment available under the DES.
The payment is worth 95p per patient and is paid when practices agree a plan for implementing the DES with their PCT.
Despite May's low uptake figure, Somerset and Dorset SHA achieved 29 per cent by the end of June, and a spokesman said this would rise to 'close to 100 per cent' by the end of July.
A spokesman for Hampshire and the Isle of Wight said uptake had risen to 46 per cent for the area in June. He said all practices would be able to sign up within the next two months.
He added that the SHA hoped to achieve the DoH's commissioning target six months early.
'We expect to be halfway to universal coverage, with all practices having received budgets by the end of this month,' he said.
The third SHA with zero uptake, Kent and Medway, reported that 'good progress' had been made despite the poor statistic. A spokesman said: 'Several practices are signed up to a PBC cluster group, so we expect the uptake to improve in the near future.'
Dr Peter Blick, Dorset LMC chairman, said that uptake had been slow because PCTs had dragged their feet.
'PCTs keep wanting applications in different formats and are very slow in agreeing practice plans for PBC sign-up,' he said.
'GPs are enthusiastic and have been frustrated at the slow progress.
PCT amalgamation is often the reason why it has been slow - they are not keen to make any financial commitments.'
The national average uptake at the end of May was 41 per cent, but some SHAs had far higher levels of interest (GP, 7 July).
South West London, South East London and Norfolk, Suffolk and Cambridgeshire SHAs all reported more than 70 per cent of practices taking up the first commissioning incentive payment.
James Murphy, PBC lead for Norfolk, Suffolk and Cambridgeshire SHA, said the area's dire financial position had concentrated PCT managers' minds on successful implementation.
'The region was split into county-wide areas to encourage sign-up. We held events early on to drive home the point that this was a high priority, especially given the financial problems,' he said.
'This is a chance for practices to be part of the solution.'
GPC deputy chairman Dr Laurence Buckman warned that DES uptake figures had 'nothing to do with commissioning'.
'We have no idea when everyone will actually hold a budget - the DoH seems to think these figures are important, but I don't think you can draw any conclusions from them,' he said.