GPs said deviating from the national agreement would stretch LMC resources to negotiate a good deal for practices, and could potentially leave them with a worse financial situation.
The motion from Newcastle and North Tyneside LMC called on the conference to reject local QOF schemes that exceed national the GP contract deal.
But representatives supported flexibility to implement new QOF measures early in some areas, so long as this does not undermine national negotiations.
Local QOF on NHS agenda
Dr Kenneth Megson from Newcastle and North Tyneside LMC said it was clear negotiating local GP contract was 'on the agenda' of NHS England.
He said: 'Local contracts would lead to local pay deals, and that would be the slippery slope, with increasing inequity of pay terms and conditions across the nation.
'This would lead to restrictions of movements of GPs, and poor areas would get poorer.'
GPC could be undermined
'GPC would be undermined with local negotiation with parts of the national contract.'
He added that it could lead to postcode lotteries of treatment for chronic diseases.
Dr Megson concluded: 'General practice needs the security and protection of a national contract.'
Earlier this year, GPs in Somerset were set to opt out of nationally-agreed QOF arrangements and replace them with their own locally negotiated scheme from April.