José Manuel Durao Barroso last weekend, citing Spanish hostility to the former Serbian province, said it would be "extremely difficult if not impossible" for Scotland to join the EU.
However, Mr Barroso's vice president for justice, fundamental rights and citizenship, Viviane Reding, today said Scotland was "nothing like Kosovo".
European Commission spin doctors have already tried to backtrack from Mr Barroso's remarks, stressing the Portuguese Conservative's remarks were not a "perfect analogy".
Ms Reding, a strong European federalist from Luxembourg, made it clear why.
She told Barcelona daily La Vanguardia: "Because Kosovo did not leave a country that was a member state of the European Union, it can't be compared."
In her interview Ms Reding made it clear she did not want to see the European Union shed any territory if parts of member states were to go independent.
"I do not want to lose Catalonia," she told the paper.
Ms Reding has previously sounded more conciliatory to "separatist" movements in the UK and Spain than some more hostile voices on the continent.
When asked about Mr Barroso's remarks, made on the Andrew Marr show last weekend, she said: "In these issues you have feelings on one side and laws on the other.
"If people, if a majority feel something, that they want to be independent, or whatever, you have to respect that.
"Such sentiments can be deeply rooted and you have to show a lot of understanding for that.
"But obviously you then have a legal situation that has been the same for decades.
"The EU is a union of member states and if anyone breaks away with one of them, they will no longer be in the union. That is a neutral response and one that counts for any territory."
However, she signaled that entry for Scotland - or Catalonia - could be easier than for countries currently outside the EU and asking to join.
She said: "Perhaps when you apply to join and you already have the same level of preparedness as actual member states on issues like the economy and justice...that could accelerate and facilitate matters. But it would be a long process."