Human error and failures in management systems have been blamed for the loss of official documents detailing everyone who voted in a crucial by-election.
But a report found there was "no malicious intent" over the disappearance of the marked register after the 2008 vote in Glenrothes.
An investigation was launched in February after it emerged that the register from November's by-election - in which Labour secured a shock victory - had disappeared from Kirkcaldy Sheriff Court.
Today Eleanor Emberson, the chief executive of the Scottish Court Service (SCS), said the report revealed "significant failings" in how the documents from the by-election were handled.
And she said: "The loss of this important register is unacceptable and I apologise wholeheartedly for the failure to safeguard these documents."
However, Ms Emberson added: "The report did not find any evidence of malicious intent in the loss of the documents or the handling of the request and notes that during the course of the investigation, no-one had suggested that the loss of the marked electoral registers casts any doubt about the result or conduct on the day of the poll."
Labour's Lindsay Roy held the Glenrothes seat - which is next door to Prime Minister Gordon Brown's Kirkcaldy and Cowdenbeath constituency - despite predictions that the SNP would win it.
When the by-election was over, Nationalists asked to see the marked register - which shows exactly who voted, as officials cross out the names of those who cast their vote at the polling station.
But at the end of January they were told this had gone missing from Kirkcaldy Sheriff Court.
The SCS brought in Bill McQueen, formerly the deputy chief executive of the Crown Office and Procurator Fiscal Service, to carry out an investigation.
Sheriff clerks have had responsibility for retaining electoral records after elections. And the report said it appeared to be the first time such documents had gone missing from a court.
The report said: "The investigation has not found the missing records and is not able to determine precisely when and how the documents came to be lost.
"It concludes that a combination of human error and weaknesses or failures in management systems and work processes at the sheriff clerk's office in Kirkcaldy caused the loss."
Tricia Marwick, SNP MSP for Central Fife, said the report left a number of questions unanswered.
With the register still missing, she added: "In the absence of these documents, it is impossible for anyone to say if this was a fair or unfair election."
However Labour hit back, pointing out that the SNP administration was itself responsible for the SCS.
Claire Baker, MSP for Mid Scotland and Fife, accused the SCS and the Scottish Government of "serious incompetence".
Ms Baker said the report made it clear "the blame for losing the register lies squarely with the Scottish Courts Service, an agency for which Kenny MacAskill and the SNP Government are responsible".
