Deputy First Minister Nicola Sturgeon has told MSPs that an independent Scotland remaining as a member of the EU was a realistic prospect.
In a statement to the Scottish Parliament, she said it was overwhelmingly in the interests of the EU for the country to remain a member.
Opposition parties had urged the Scottish government to make their position on Europe clear.
They said recent comments by the EC's president had cast doubt on the issue.
Jose Manuel Barroso told both the BBC and a House of Lords committee that a new member state would have to reapply to join the European Union.
Ms Sturgeon said common sense should prevail and it was in the interests of Scotland, the EU and the UK for Scots to remain in Europe.
She told the chamber that it was important to be respectful to the head of the commission, but she added that Mr Barroso was not the final arbiter on the issue.
The Scottish government says, if Scotland voted to become independent in the 2014 referendum, it would continue within the EU and negotiate membership terms between then and the 2016 Scottish election.
Ms Sturgeon answered a number of questions from MSPs, including Labour's Patricia Ferguson and former Scottish Tory leader Annabel Goldie.
During her address to the chamber, Ms Ferguson said that in 2007 Ms Sturgeon said it was a "clear view" that Scotland would "automatically" be a member of the EU on becoming independent.
She said the SNP minister also said at the time that there would be "no" requirement to negotiate.
Ms Ferguson said that by First Minister's Questions in September, Alex Salmond said there must be negotiations. She added that in the same month, the Yes Scotland independence campaign said it was common sense that an independent Scotland would remain in the EU.
The MSP said: "Now today, in her statement, the deputy first minister simply talks about a vague intention to remain in the EU.
"First it was automatic, then we needed negotiations, then it was common sense and now it's an intention.
"But of course all of this, and much of her statement today, is mere assertion."
Tory Ms Goldie described Ms Sturgeon's insistence that Scotland would continue within the EU as "a triumph of optimism over hard headed facts".
The minister said: "My statement is based on common sense and realism and I think most people, other than those gripped by the fevered imagination that grips the better together Labour/Tory Liberal alliance, would recognise the realism at the heart of what I said.
"Is Annabel Goldie, or anyone else in this chamber, seriously saying that Scotland would find itself ejected from the European Union - oil rich, renewable energy rich, fishing rich Scotland."
Earlier, during first minister's questions, Mr Salmond told MSPs: "The country with 90% of the oil reserves of the European Union, with 25% of the potential renewable energy reserves, the second-largest gas provider in the European Union with 60% of the territorial waters of these islands is something that no serious person across this continent would try to exclude from the European Union."
Labour, the Conservatives and Liberal Democrats have said the Scottish government argument is based on "meaningless assertion" and lacks legal evidence.
Ms Sturgeon had written to the European Commission asking for early talks on the matter.