Both the BMA and the RCGP complained that many SHAs' care pathway groups were dominated by professional executive committee (PEC) members and contain few or no ordinary GPs.
Each SHA was asked to set up groups to discuss eight core clinical pathways, in order to feed back their conclusions for the final stage of Lord Darzi's review of the NHS.
The BMA was allowed to nominate doctors who would provide expertise to each of the groups, but many were not included.
Yorkshire and Humber SHA in particular fielded no BMA-nominated GPs.
Dr Russell Walshaw, chief executive of East Yorkshire and Lincolnshire LMC, said four very good GPSIs were ignored in favour of GPs with PCT links.
'When we looked closely at the names we found the groups were predominately made up of PEC chairmen and medical advisers to PCTs. It didn't seem to represent your average, working, non-political GP,' he said.
'We think it's a bit of a sham. The Darzi review looks predetermined and just representing the PCTs' view. It's just one more bit of evidence that the results of the review are already decided.'
GPC deputy chairman Dr Richard Vautrey said: 'It will be very interesting to see if different areas come to different conclusions. They may have been given the blueprint already.'
RCGP chairman Professor Steve Field said: 'In discussion about quality of care you should look outside your normal management structures.'
Professor Chris Welsh, clinical champion for the 'NHS next stage review' in Yorkshire and Humber, said: 'Given the need to limit the size of the clinical pathway groups we have not been able to include all of the names put forward by a large number of professional groups and others.'
He said that a separate group of primary care experts had been established to advise the care pathway groups.
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