Motions backed by the UK LMCs conference in central London on Friday called on the GMC to 'reaffirm' that GPs' primary responsibility is to their patients and not financial balance.
They also warned that a new system of incentive payments for CCGs, dubbed the 'quality premium', threaten GPs' professional, independent role as their patients' advocate.
Dr Jerry Luke from West Sussex LMC, who proposed the motion, said he had recently resigned as medical director of Crawley CCG, in part over fears that all CCGs would have to make service cuts, which would affect patient care.
He said CCGs only have 'one real duty and that is to end the year in budget'.
'CCGs are not allowed to run out of money,' he said. 'They can run out of services, but they cannot run out of money.
'I fear without the GMC telling us time and again that our patients have to come first, before the money, then we are going to be led by some of our colleagues who are quite happy to cut and slash just like the DH wants. I personally am not prepared to carry on like this.'
Dr Luke warned that GPs could be held accountable for decisions taken by CCGs.
He explained: 'NHS organisations always go over budget. Senior managers move on, the new chief executive says, "I wasn't there at the time, you can't blame me". The money is found somewhere and the thing still keeps going round. Well, that isn't going to happen anymore. As GPs we don't just pick up sticks and move. We stay in our communities.
'Accountability stays with the whole membership and that is all of you, my friends. You cannot get away from these decisions unless you relinquish your NHS contracts.'
The motion called on the GPC to ensure that 'colleagues who are keen commissioners are aware that putting financial targets ahead of clinical priorities will lead to more patients feeling "we have an NHS that just does not care".'
It also warned that the quality premium - the payment made to CCGs if they reach certain targets - risks 'destroying the trust patients have in their GP to make decisions based on their best interests not as a result of a financial incentive'.
Dr Luke told GP that he resigned from his CCG role this month because of a rise in both practice workload and the bureaucracy involved in clinical commissioning.