Ruth Davidson, leader of the Scottish Conservatives, criticised the move for a second vote saying that SNP is "hell bent on taking Scotland back to another divisive independence referendum and will use any excuse to do so".
"But let me be very clear we don't see any need for another referendum we had one just two-and-a-half years ago, it was accepted as a clear cut result at the time and there is plenty of other business for the Scottish government to be getting on with".
The first minister has made clear that, if Scotland is unable to retain membership of the EU or the European single market, an independence referendum will be held to ensure Scots - who voted to Remain in the EU - have another choice.
"I'm not ruling anything out".
Mr Swinney told Ms Davidson that the then Prime Minister had promised in 2014 that Scots would benefit from a £200bn oil boom if the voted No - and that rejecting independence would be the best way to secure the country's place in the EU.
Ministers are said to believe it is a case of when, not if, they are called to vote on the issue.
No decision has yet been taken on a date for a vote, she added.
If Mrs Sturgeon is to consider holding a referendum next autumn she would have to announce that at least nine months before it could be held.
First Minister Nicola Sturgeon is indicating the country's likely to have another vote next year on whether it wants to stay in the UK.
In contrast, 26% strongly disagree with the idea of a second Brexit referendum while 14% tend to agree, with 6% who neither agreed nor disagreed and 2% who said they did not know.
The SNP leader has also described a referendum in autumn 2018 as being in a "common sense" time period during the negotiations between London and Brussels.
"Too much of the way in which the campaign was fought allowed to be characterised as a contest between governments in Holyrood and Westminster".
"If Scotland decides to proceed with the second referendum to quit the United Kingdom, there would certainly be another fundamental downshift in the pound's value, both against the USA dollar and the euro".
There is speculation that Sturgeon may announce a second referendum at the SNP conference next weekend (17-18 March). I suggested that Sturgeon's sense of urgency might be explained by opinion polls showing her "tanking" approval rating.
Scotland voted 63 per cent to stay in the European Union in the historic referendum.