The decision to block release of the internal "risk register" on the 2014 poll means voters will not be able to find out the potential hazards flagged up by Scottish Government civil servants.
The refusal to publish – which Labour has put down to the SNP's "secrecy obsession" – will now be investigated by the country's Information tsar.
Risk registers, which are compiled by government bodies to outline the dangers of policies, shot up the political agenda last year during the debate over the UK Government's controversial health legislation.
Health Secretary Andrew Lansley declined to hand over the register for a Bill that laid the foundations for sweeping changes to the NHS.
However, the UK Information Commissioner then ruled there was "considerable public interest" in disclosure, while the Information Tribunal also ordered release.
Lansley wielded his FOI veto to block publication, arguing that Ministers needed a "safe space" in which to conduct policy.
Now the Scottish Government finds itself embroiled in a similar row after the Sunday Herald asked Ministers for a copy of all risk registers on their policy of holding a constitutional referendum.
Although the Government confirmed holding the documents, the request was turned down on the grounds that Scottish Ministers required a "private space" for seeking advice. The SNP government has no intention of publishing the risk register before the independence referendum is held.
The response added that the benefit of the risk "process" could only occur "if the risk register includes all possible risks, however unlikely it is that some of them may be realised".
An internal review of the decision also backed secrecy, with officials noting that the register was an "assessment ... based on what might hypothetically happen rather than fact".
The review, conducted by an official in the Government's International Division, concluded that it was in the public interest for Ministers to receive advice "which includes a comprehensive assessment of all risk".
The register is likely to dwell on the legality of the Scottish Parliament being able to stage an independence referendum.
UK Ministers believe a plebiscite can only be organised by Holyrood if the specific power to do so is devolved, whereas the Scottish Government is adamant the power is already within the Parliament's gift.
The dispute over the public release of the risk register will be adjudicated on by Scotland's new Information Commissioner, Rosemary Agnew. If she orders publication, Ministers could challenge it in the courts.
The First Minister also possesses a veto, but this is a nuclear option that he can only use if the information is deemed to be of "exceptional sensitivity".
The decision to block release of the risk dossier comes amid fears the Government is taking an unduly conservative attitude towards Freedom of Information (FoI) legislation and the constitution.
It was revealed recently that civil servants had been invited to attend two "constitutional reform" seminars on FoI.
An advert noted the sessions would list "the steps that should be taken in responding to FoIs, using FoIs we have already received on constitutional reform as case studies".
It emerged last month that the Government had refused to confirm or deny whether it held legal advice about an independent Scotland's membership of the European Union.
The Information Commissioner, in a landmark decision, ordered Ministers to reveal whether the advice exists.
As an MP, Salmond was a strong voice for open government, and regularly called on the previous Labour government to release the secret legal advice it received prior to the invasion of Iraq.
Sir Alistair Graham, the former Chairman of the Committee on Standards in Public Life, said: "There is nothing the public hates more than hypocrisy. If there is seen to be a difference between Alex Salmond's demands earlier in his career and the way he has acted as a Minister, then the public will take a very dim view of this matter."
Patricia Ferguson, Scottish Labour's Shadow Cabinet Secretary for External Affairs, said: "At every turn, the SNP are determined to keep the details of separation from the Scottish people and Salmond's secrecy obsession is becoming more worrying by the day."
Green MSP Patrick Harvie said: "Sadly the SNP's general attitude towards FoI leaves a lot to be desired."
Scottish LibDem leader Willie Rennie said: "People need to know the risks involved around the independence debate but the SNP would prefer to keep them in the dark."
A spokesman for the Scottish Government said: "The Scottish Government is committed to proactively publishing information whenever possible – this decision is fully in accordance with Freedom of Information legislation."