The experiment, which was the brainchild of former health secretary Nicola Sturgeon before she took charge of the independence campaign, aimed to give the public a louder voice in the way hospitals and health centres are run.
But new figures show the enormous cost of the operation after just 39,761 people, or 14% of the population, in Fife cast their votes at a total cost of £473,856 (£11.90 a vote).
Ms Sturgeon's successor Alex Neil is now deciding on the next step as the Government digests the huge costs of mounting a Scotland-wide vote.
But Labour's health spokeswoman Jackie Baillie said the trial was disappointing as it had done nothing to improve the accountability of health boards.
She said: "The election trial was extremely disappointing with a poor voter turnout and no real improvement in accountability of health boards.
"Yet, despite this, the SNP wish to press ahead, wasting £12m on elections which few understand and even fewer will participate in, rather than investing in frontline patient care.
"There is no evidence the trials have led to better management, more efficient services, or better patient care. In a time when there are cuts to the health budget, it seems the SNP have the wrong priorities in pushing this agenda."
In Dumfries and Galloway, the turnout was higher at 22.6%, but the 26,516 votes cost £299,406 to administer, around £11.30.
The poll was important in the run up to the independence referendum next year because it gave those aged 16 and 17 the vote for the first time in a UK poll. The age group could also stand as candidates, but even before it had taken place there was criticism over the costs from health boards, staff unions and even consumer groups.
Dr Charles Saunders, deputy chairman of the BMA in Scotland said an analysis had shown that less costly pilot elections in Grampian and Lothian had produced similar results in terms of numbers of votes cast.
He insisted: "At a time when clinical staff and health services are feeling the pressure of the financial cuts to the NHS, it is more important to invest in frontline services rather than elections which have a poor turnout and don't deliver any significant difference to far cheaper alternatives."
He added: "Elected members tell us they feel their role is to effectively rubber stamp decisions made by the executive members of the board, rather than to proactively involve themselves in the decision making process.
"It is doubtful that, as a result of these elections, the average person in Fife or Dumfries and Galloway feels there is greater transparency about the decisions made regarding healthcare services in their local communities. It is our view improved engagement is best done at the most local level."
Mr Neil confirmed it would cost around £12m to extend the pilot to the rest of the country and said: "The Scottish Government will take this information in to account as it considers the independent evaluation on health board elections and alternative pilots."