Cambridgeshire LMC proposed that the voluntary levy which pays for the fund should be varied between the UK's four nations, so that money can be directed to where it is most needed.
They pointed to variation in healthcare spending and prescription charges as evidence that GPs face different threats across the four countries.
But GPs from Scotland and Wales argued that the motion posed a threat to the profession's unity.
‘We have the same contract. It needs to be defended jointly,' said Dr Mike Griffiths, from Gwent LMC.
Dr John Ip, from Glasgow LMC, added: ‘Politicians would love us to start squabbling over this.'
Conference declined to vote on the motion.