Professor Stephen Tierney stepped down as a Government expert adviser to work for Parliament's Referendum Bill committee, set up to examine ministers' plans for the vote.
He was to have advised on the design of the ballot paper, the wording of the question and structure of the referendum. But he said he preferred to work for the cross-party committee, as there was "less room" for his role to be politicised.
Mr Tierney, professor of Constitutional Theory at Edinburgh University, said: "A clear condition was I had no connection to the executive. I want to make clear what I did in relation to the Government – not much."
Mr Tierney said he had no direct dealings with ministers and produced one paper for the Government on multi-choice referendums, yet to be published.
He was brought in by Mr Salmond as an unpaid independent expert adviser in July after warning a multi-question referendum would be "tricky" to devise.
Mr Salmond said he would help ensure the referendum met the highest international standards.
A Scottish Labour spokesman said: "The SNP appointed Stephen Tierney as they thought he would do their bidding.
"When he refused, he was pushed to one side and realised his appointment was a fig leaf which hid the SNP's desire to ride roughshod over anyone who disagrees."
* MSPs will have less than four months to pass new laws allowing 16 and 17-year-olds to vote in the referendum, papers considered by the Referendum Bill Committee said yesterday.