Deputy First Minister Nicola Sturgeon called for urgent talks with the commission last week after its president suggested a newly independent Scotland would need to apply for EU membership.
The comments by Jose Manual Barroso contradicted the SNP's long-standing claim that Scottish entry would be automatic after a Yes vote, and that Scotland would inherit the UK's opt-out from the euro and the open-border Schengen travel area.
Although the issue is devolved, until now there has a common system on both sides of the Border.
Writing in the Sunday Herald today, the First Minister says it is "unarguable" that there should be separate Scottish reforms, and suggests "light touch legislation" will be required.
But the three Unionist parties vehemently attacked the idea, with Labour even suggesting Salmond only wanted the means to "bully and intimidate the Scottish press" in the run-up to the independence referendum.