Scotland's future is part of an ongoing constitutional debate
The Scottish government plans to set up a special body to run a future referendum on independence.
Ministers do not want to use the Electoral Commission which overseas Westminster elections.
The plan was revealed in minutes of meetings which were obtained by the BBC under Freedom of Information.
The draft bill on the independence referendum - which could take place as soon as 30 November - is expected to be published on Friday.
Extracts from correspondence between the Electoral Commission and Scottish government officials
Email from the Scottish government, 13 March, 2009 - "We are now looking at what the question in an independence referendum might be and at some point will need to show we have properly assessed it for intelligibility, neutrality, etc."
Electoral Commission minute, 22 September, 2009 - "Scottish government officials confirmed... that there was currently no provision to consult any organisation as to the intelligibility of the referendum question."
Electoral Commission minutes, 6 November, 2009 - "There seems little regard to the remit and role of what the Scottish Referendum Commission would actually do."
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The Electoral Commission has a statutory role to run referenda called by Westminster, but has no formal role in those called by the Scottish Parliament.
In the minutes obtained by BBC One's Politics Show, civil servants told the commission they planned to set up a new body - the Scottish Referendum Commission - to run the election.
The paperwork also revealed the concerns of the Westminster commission over the wording of the questions and that the timescale towards the poll was too short.
A minute from September last year said: "Scottish Government officials ... confirmed that there was currently no provision to consult any organisation as to the intelligibility of the referendum question".
No Scottish minister would comment on the FOI minutes, however, a spokesperson said that Scottish voters already had quite recent experience of a multi-option constitutional referendum.
The Electoral Commission said that when the government sets out the referendum on full independence, it would "consider it and submit a response" using experience of planning for referendums in the UK.
'Waste of time'
It added: "We are not able to comment until this public consultation is opened."
Commenting on the revelations, Scotland's Tory leader, Annabel Goldie, said First Minister Alex Salmond's "separation bill" was a "monumental waste of taxpayers' money and would fail".
She added: "Instead of dreaming up new ways to rig a referendum, Alex Salmond should get on with what he was elected to do."
Scottish Labour's Pauline McNeill said the "revelations expose how the SNP is trying to rig a referendum by getting round the rules".
She added: "While the rest of the world is trying to get people back into work and create jobs, Alex Salmond is wasting time and money on a doomed referendum plan.
"The Electoral Commission is there to be the neutral referee.
"By ordering the referee off the pitch, Alex Salmond is trying to avoid the scrutiny."