Labour's Lindsay Roy held Glenrothes in the by-election
An independent investigation is being carried out after marked electoral registers for the Glenrothes by-election were lost by the courts.
The registers, which are the only record of who voted in the Westminster election, must be kept for a year.
Tricia Marwick, Nationalist MSP for Central Fife, said the blunder was "beyond belief".
Labour comfortably saw off an SNP challenge to hold the Glenrothes seat in November.
The Scottish Court Service described the incident as "deeply regrettable" and confirmed an external investigation would be carried out into the incident.
Fife Council said it had a receipt proving the authority handed the electoral registers over to the sheriff clerk at Kirkcaldy.
Lindsay Roy held on to the seat for Labour with a majority of more than 6,000 in the by-election, which was held following the death of sitting MP John MacDougall.
Ms Marwick called for an independent inquiry, adding: "It is almost beyond belief that a by-election which attracted media coverage throughout the UK, which delivered such a surprise result and had a much higher turnout than anticipated, now has no records to show who actually voted."
Scottish Labour backed calls for a probe into why "an SNP government department lost confidential personal data again".
A spokesman for the party added: "Lindsay Roy won the by-election because of the incompetence of the SNP locally and nationally.
"The ballot papers were counted fair and square in front of the eyes of the world."
Scottish Court Service chief executive Eleanor Emberson, said: "It is important for all concerned to establish what happened to the marked register.
"I deeply regret and apologise for this loss and am arranging for the matter to be fully and independently investigated."