The call from University of Aberdeen professor Dr Philip Wilson came as a poll by the Rural GP Association of Scotland (RGPAS) found that almost 90% of members had voted against the proposed new contract, or planned to do so.
Voting on the new Scottish contract is due to close on Thursday - with GPs given from 7 December to 4 January to have their say. Results of the ballot are expected to be published on 18 January as the Scottish GPC meets to discuss the votes and choose whether to implement the new deal.
Professor Wilson wrote to the BMA, the Scottish government and the Electoral Reform Society - which is conducting the ballot - on 31 December to highlight his concerns.
He criticised the decision to enclose a document that 'appears to be designed to elicit agreement with the terms of the new contract' alongside ballot papers posted out to GPs across Scotland. 'I have never before received a ballot paper from the Electoral Reform Society along with a document encouraging me to vote in only one way, in the same envelope,' he wrote.
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The Aberdeen academic also criticised the evidence underpinning plans to revamp the GP funding formula under the new contract - a move that has left rural GPs in Scotland warning that they could face 'extinction'.
'Unreasonable' assumptions around practice workload informed proposed changes to the formula, Dr Wilson says.
The letter came just two days before the RGPAS published findings from a poll of its members, which found that 89% had voted against the deal or planned to do so. Of 115 RGPAS members, 65% voted - with only 11% of these backing the new contract.
GPonline reported last month on a poll of members of the campaign group GP Survival in Scotland - which also found substantial opposition to the contract.
Just 31% of GP Survival in Scotland members planned to back the contract, while 43% planned to oppose it, with the rest undecided.
GPC Scotland chair Dr Alan McDevitt said: 'While Professor Wilson is entitled to his own views on the proposed GP contract, the poll will allow the whole of the profession in Scotland to have their say.
'The proposed contract is a significant step forward for the whole of general practice in Scotland, helping to substantially reduce business risks to GPs and return workload to sustainable levels.
'Like any major change, there has been a lot of healthy debate and discussion as we have engaged with GPs across the length and breadth of Scotland to explain what these proposals would mean for them.
'As the poll comes to a close, I am looking forward to hearing the feedback of the profession and their view of whether the contract should be implemented.'