Holyrood wants to seize control of negotiations for three quarters of the GMS contract, citing irreconcilable differences with the NHS reforms in England.
GPonline.com understands this would involve a large-scale rethink of the QOF in Scotland, with big changes planned for the framework to refit the scheme for Scottish GPs.
It could affect up to 40% of QOF points, including the controversial quality and productivity indicators.
GPC Scotland chairman Dean Marshall told GPonline.com: 'The Scottish government's view is that the health agenda is so diversified across the UK now that it causes difficulties for the UK contract.'
He said the Scottish government's proposals would retain the UK contract but seek to increase the 'flexibility' to tackle public health issues prioritised in Scotland, such as alcohol abuse.
'What it's said to us is: it wants to maintain a UK contract but increase the flexibility to do [things] differently,' he said.
Asked whether the move signalled the beginning of the break up of the GP contract, Dr Marshall said 'Time will tell.'
Scottish health secretary Nicola Sturgeon said: 'My proposal is not to recast the structure of the contract but instead to repatriate aspects of the annual negotiation in order to introduce change in some important areas - in particular public health and the standards of care set out in the organisational indicators - and to leave on a UK basis the indicators for good clinical care.'
GPC Scotland said it believes the Scottish government will seek to transform indicators relating to the current organisational domain - which includes records, education and medicines management - to reflect differing priorities in the country.
This would involve Scotland negotiating its own terms for the controversial new quality and productivity (QP) indicators, which also form part of this organisational domain.
The QP indicators were introduced by the DH in 2011/12 to meet England's £20bn efficiency drive under the Quality, Innovation, Productivity and Prevention (QIPP) programme. But plans to link A&E attendance to QOF pay from 2012 have been criticised by GPs as they may fall outside their control.
Different priorities for Scotland
Dr Marshall said the Scottish government believes these public health measures are too Anglo centric and wants its own versions to tackle what Holyrood sees as different priorities.
Repurposing organisational and public health domains to suit Scottish interests would mean around 40% of QOF would be nationally determined, outside of overall UK control.
The Scottish government has yet to confirm the details of its proposals, but said it would be consulting with the BMA over the next three months and was 'keen to hear the views of GPs from around the country'.
Earlier this month, GPC leaders in Scotland, England, Wales and Northern Ireland had said their preferred option was to retain the UK-wide deal, but that England's reforms put this at risk.
The 2011 LMCs conference in June voted to maintain a UK-wide deal.