Professor Jim Gallagher responded days after Alex Salmond quoted him in support of the case for seamless EU transition within 18 months.
But in a letter to Mr Salmond, he writes: "I have consistently said that's too short for all that needs done. Indeed, setting a fixed date weakens our negotiating hand. Imagine trying to buy a house when the seller knows you have no choice about the entry date. What happens to the price?"
Mr Salmond used his words against a challenge from Tory leader Ruth Davidson during First Minister's Questions at Holyrood.
She had said the SNP's preferred route into the EU through a treaty amendment is not legally correct.
Mr Salmond replied, quoting a blog by the academic: "It seems pretty likely Scotland would be an EU member state probably, after an accelerated set of accession negotiations.''
Prof Gallagher's letter continues: "I'm sure you didn't mean to mislead, but you should have spotted that I was talking and have only ever written about accession, not treaty amendment.
"To my knowledge, I've never written anything about treaty amendment, because it's clearly not suitable."
A spokesman for the First Minister said: "Professor Gallagher has been caught red handed telling the truth and because it doesn't suit the Project Fear script, he's trying to worm his way out of it.
"The fact is that his admission - that any requirements to join the euro or Schengen "can surely be avoided" and that Scotland's membership of the EU would be agreed in an "accelerated timetable" - have utterly undermined key scare arguments of the No campaign."