Fiona Hyslop said if that was not the case the Scottish Government is “absolutely serious” about staging a second independence referendum.
She also insisted the reaction from the rest of the European Union to an independent Scotland would not be the same as in 2014, when pro-UK campaigners insisted if the country left the UK it would not be able to gain membership of the EU.
Ms Hyslop spoke out at a fringe event at the SNP conference in Glasgow which was organised by the European Free Alliance (EFA), which brings together political parties from across Europe - including the SNP - which campaign for independence and greater self governance.
EFA president Francois Alfonsi said: “For us Scotland is definitely European, regardless of what the rest of the UK voted.
“The Scottish people, with a great majority, expressed their determination to remain in Europe.”
While the UK as a whole voted to leave the EU, almost two thirds of Scots who took part in the referendum backed staying in Europe, prompting First Minister Nicola Sturgeon to warn another independence referendum is “highly likely”.
The Scottish Government is now due to publish an Independence Referendum Bill for consultation next week.
But Mr Alfonsi insisted Scotland’s vote to stay part of the EU should be respected.
He told the audience: “In 2014 unfortunately the Scottish people voted to remain in the UK. This was respected. In 2016 the Scottish people voted to remain in the European Union and also this should be respected by everyone in the same way.
“But Theresa May and the Tories do not intend to respect the Scottish democracy.”
The Corsican politician added: “Greenland is a part of Denmark but outside of the European Union, with the same logic Europe should enable Scotland to stay in the European Union, even if the UK leaves the European Union.”
Ms Hyslop insisted SNP ministers would try to persuade the UK Government to pursue the “the least worst option” when negotiating a deal to leave the EU.
But she added: “If we can’t get that we certainly must have a differentiated option.”
Ms Hyslop stated: “If required we will pursue that independence option, we have got that opportunity, we will lay the draft legislation next week for consultation. We are serious, we are absolutely serious about protecting Scotland’s interests.”