GPC Scotland chairman Dr Dean Marshall said a UK contract remained the best option.
But he said it may no longer be viable if the Health Bill forced a change to the GP contract in England.
The Scottish LMCs conference, held in Glasgow on 10 March, was set to debate the future of the UK contract as GP went to press.
Lothian LMC tabled a motion calling for the GPC and the Scottish government to assess the feasibility of a new Scottish GP contract.
Dr Marshall said he believed NHS reform plans in England had triggered the motion.
He said England's health reforms did not require significant changes to the GP contract despite plans to alter the role GPs will play in the NHS.
But he said the English government may insist on altering the contract to reflect the changes, and this could make it 'extremely difficult' to maintain a UK contract. 'We are not looking to have a separate contract, but we might be pushed into a position by England going a separate way,' Dr Marshall said.
But he warned it would be difficult for both governments to run and negotiate separate contracts. 'The workload involved would be significant on both sides,' he said.
Meanwhile, Dr Marshall said whether to introduce GP commissioning in Scotland was another key issue for debate.
Grampian LMC will call for 'some form of GP-led commissioning' in Scotland. But Ayrshire and Arran LMC has tabled a motion opposing GP commissioning in Scotland.
Dr Marshall said he would like to see GPs more involved in decisions, but neither the government nor GPs wanted a market-based NHS in Scotland.
Other motions set to be debated include a call for Scottish GPs' pay to match the other three countries of the UK.
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