GPC leaders have admitted that the square rooting mechanism in the prevalence formula used to weight quality pay 'overcompensates' for differences between practices.
LMCs representatives carried motions calling for changes to make the prevalence formula reflect workload.
Dr Ashok Rayani from Morgannwg told the conference that GPs in Wales have to work harder and pay more staff because of higher levels of disease.
Prevalence in Wales was now 15 per cent higher on average across domains of the quality framework compared to 10 per cent last year, Dr Rayani said.
The average Welsh practice would be around £5,000 better off in England, he added.
These losses were compounded by enhanced services cuts averaging £9,000 per practice and the pay freeze, which meant some Welsh practices were 'being pushed to the brink of viability'.
GPC deputy chairman Dr Laurence Buckman said: 'It is unfair that Welsh doctors have to work harder for the same pay. The negotiators are looking at that now.'
He added that the square root formula had gone too far in trying to avoid huge variations in pay between practices: 'What we now know is that the square root formula actually over-damps the differences between practices.'
Changing the deal could create new winners and losers, Dr Buckman said, but this was 'not a reason not to do it'.
Meanwhile, LMC representatives also voted that the GMS contract has failed to direct resources to areas of greatest need and deplored this failure.
However, they rejected a motion calling for 'most available new money' to be directed to these areas.