An independent Scotland's border arrangements with England would be determined by EU rules, Mike Russell has said.
It further raises the prospect of a "hard border" between Scotland and England if Scots vote to leave the UK and rejoin the EU.
Read more: Nicola Sturgeon refuses to rule out 'hard border' with England in event of Scottish independence
The Scottish Government's constitution Secretary said his officials are currently "re-examining" the 35 articles of accession for EU membership to ensure that Scotland "measures up" after an independence vote
"The position of the Scottish Government is to seek independent membership of the EU," he told a Law Society of Scotland Fringe event at the SNP conference in Aberdeen today.
"That is what we seek to do, that is what we are going to do."
If the UK pursues a different policy on tax and trade tariffs after leaving the EU, while Scotland rejoins the Brussels bloc, many experts believe a border will be inevitable.
Mr Russell added: "There will be issues that will confront us as an independent country which we will have to recognise and respond to.
"The issue of the relationship between countries and borders between countries, of course, will be an issue.
"But it will be governed by our membership of the EU, that is the important issue - just as Ireland's relationship with the UK will be governed."
Read more: Poll: Support for Scottish independence hits 50%
Nicola Sturgeon yesterday refused to rule out the prospect of a hard border between Scotland and the rest of the UK after independence.
Nationalist MEP Alyn Smith hinted that Scotland could follow other border regimes which already exist between the EU and its neighbours.
"If the border looks like Northern Ireland, if the border looks like Sweden to Norway, if the border looks like France into Switzerland there are exemplars that already exist and the EU is looking at this stuff as well," he said.
But the prospect of a border has come under fire from pro-unionpoliticians.
Labour leader Richard Leonard said: "Whether it's a hard border or the hard cuts of the so-called Growth Commission, the SNP has shown it is determined to pursue a separate state even if it badly hurts the people of Scotland.
"A hard border between Scotland and England would cost jobs, hurt our public services and divide families. Our communities don’t need more barriers and disruption. That’s why Scottish Labour wants to remain in - and reform - both the UK and the EU. We want to end the constitutional crisis, not create another one. And we believe our vision for a radical transformation can appeal to people who voted both Yes and No to independence in 2014."
Tory finance spokesman Murdo Fraser said the case for independence has "never been weaker."
He said: “Not only have the nationalists repeatedly failed to address the issues surrounding currency and how to plug a black hole worth billions of pounds. Now we have Nicola Sturgeon admitting a hard border could be put up if her plans to break Scotland away from the rest of the UK come to fruition.
“All of this would make Scotland poorer, our businesses less competitive and put hardworking Scots right up against it."