The affiliates, whose job was to support employers concerned about doctors' performance, significantly improved the 'efficiency and effectiveness' of complaints handling, according to accountants KPMG.
The firm evaluated one-year schemes in north and central London and west Yorkshire.
The affiliates worked in pairs, one an experienced fitness-to-practise GMC employee, the other a doctor.
CMO Sir Liam Donaldson angered doctors in 2006 when he said there should be a GMC affiliate in every PCT as part of the post-Shipman reforms.
But the model evaluated by KPMG spreads the affiliates more thinly, with 35 pairs covering England.
The affiliates 'greatly improved' the relationship between the GMC and medical directors and improved their knowledge of fitness-to-practise thresholds, KPMG reported.
They also helped to settle complaints against doctors more quickly.
But the model, a 'gold standard', could cost £7.4 million to roll out and £4.5 million a year to run. No one has decided who would pay for it.
The DoH and the GMC are now examining cheaper alternatives, dispensing with the medical affiliates or even scrapping the scheme altogether.
Dr Kailash Chand, chairman of NHS Tameside and Glossop and a GPC member, said that unless extra money has been identified to pay for the affiliates scheme, its success is 'neither here nor there'.
'If PCTs have to put money aside for this, it will affect patient services.'