One in 10 of these practices had to challenge their PCT to receive payment, Freedom of Information responses from 115 PCTs show.
GPs were paid £5.25 per vaccine for delivering swine flu jabs. Practices achieving uptake levels above 50.7% were rewarded with reduced thresholds for QOF patient experience indicators. But just 14% of practices benefited from this easement.
Source: GP investigation.
In total, 21% of practices achieved uptake above 50.7%. But around a third of these (7%) had already exceeded the original patient experience threshold and so received no additional pay.
GPC deputy chairman Dr Richard Vautrey said a straightforward per-vaccine payment would have been 'far more sensible'. But he said the DoH had been keen during negotiations to limit the headline figure GPs were paid because of how it might play in the media.
'They were being led by the Daily Mail and that's no way to develop policy,' he said.
The DoH and the GPC are currently negotiating 'sleeping contracts' for delivering vaccines in future pandemics.
Dr Vautrey said the GPC would be seeking a straightforward deal. 'The best way of supporting us is to have a pay-per-vaccine system as we do for seasonal flu,' he said.
Dr Jane Lothian, secretary of Northumberland LMC said the swine flu deal was 'perverse'.
'A vaccine is a vaccine,' she said. 'It would have been much better to have been paid for doing each jab.'
Dr Peter Higgins, chief executive of a consortium of LMCs in Lancashire and Cumbria, said the deal caused 'all sorts of problems', and discussions with PCTs had been 'hard work'.
Suffolk LMC vice-chairman Dr Christopher Browning said ad hoc vaccination programmes involved paying for additional staff and consumables.
He said a pay-per-vaccination deal gave 'a clear relationship between additional work done and remuneration'.