BMA GP committee chair Dr Hamish Meldrum told members that the practices were being pressured to sign up to the general medical services contract.
He told the annual conference of the BMA's local medical committees: 'This present witch hunt by certain PCTs is not only unfair to practices, it seriously risks damaging services to patients.'
Dr Meldrum, the favourite to be elected as BMA chair on 28 June, said that re-negotiations had been fought off by practices sticking together.
He added: 'We would like to see a national framework for a fair return to general medical services but, until then, local unity.'
The conference also carried a vote of no confidence in the government's handling of the NHS and in health secretary Patricia Hewitt.
He berated PCTs for the 'extreme measures taken to try to save their own necks and Patricia Hewitt's job', citing delayed operations and outpatient appointments, redundancies, ward closures and the slashing of training budgets.
The committees also voted that the reconfiguration of PCTs had failed to deliver intended management savings or improvements, demoralised managers and clinicians and caused 'organisation stagnation and planning blight'.
The conference also voted for GP pay negotiations to continue to go through the Doctors' and Dentists' Review Body, following the collapse of talks with NHS Employers.
It voted against industrial action but called for the GP committee, along with LMCs, to develop a local and regional plan to empower practices to limit their workload.