Just 13.9% of eligible people turned out to vote for members of the local health board in NHS Fife, part of a pilot costing £2.5m.
GPC deputy chairman Dr Richard Vautrey said: ‘I think we should question the value for money of such schemes. While laudable, they are expensive and if they take away resources from frontline services they may be of questionable value.'
The BMA said the pilot elections showed there was ‘little appetite' for such elections.
In early June, NHS Dumfries and Galloway and NHS Fife held the first elections for members of the local health board, part of a two-year pilot scheme in Scotland. Two 'non-statutory' alternatives will run in Lothian and Grampian.
But just 22.4% of the electorate turned out to vote in NHS Dumfries and Galloway, and just 13.9% voted in NHS Fife.
The coalition government's manifesto pledges to roll out elections for local NHS boards across England to increase local accountability in the NHS.
The BMA said the elections were a waste of money and not representative of the local population.
Dr Brian Keighley, chairman of the BMA in Scotland, said: ‘At a time of economic hardship, the health spending budget is better spent providing vital services to the local population rather than a costly election process which has received a less than desirable turnout.'
The BMA was concerned that those elected as members may use the position for political purposes.