Jim Currie told MSPs that Scotland would have a right to be an EU member and other states would not attempt to block this.
The former mandarin was appearing before MSPs on Holyrood’s European committee yesterday.
The EC President sent shockwaves through referendum debate at the weekend when he warned it would be “extremely difficult, if not impossible” for Scotland to re-negotiate its way back into the EU after independence.
But Mr Currie said: “I think he was unwise to express the opinion he expressed in terms of the virtual impossibility of Scotland becoming a member state of the EU.
“I think that was extremely unwise.
“I don’t think he was correct and I don’t necessarily think that opinion is shared either among all the member states or even necessarily within the Commission.”
Mr Currie said it was unclear whether Mr Barroso was speaking on behalf of the Commission or as an “outgoing President” of the Commission.
Mr Barroso compared Scotland’s situation with Kosovo, but Mr Currie said a more appropriate parallel would be German unification where the political situation required a degree of pragmatism. In the event, East Germany was incorporated into the EU in a matter of months “Kosovo was an unfortunate example,” he said.
“Scotland already has been applying the highest principles of democracy and human rights.”
He added: “We would be talking about a territory which is currently part of a full member state. We’re dealing with people who would have certain rights as EU citizens and which would be very difficult to take away, and nobody would want to.
“The bottom line for me is that it would be dealt with in a pragmatic way, and it would involve inevitable negotiations which would be rather tough.”