His comments came during an interview with the BBC, and Barroso said Scotland would have to apply for membership and get the approval of all the current member states.
"We have seen Spain has been opposing even the recognition of Kosovo, for instance. So it is to some extent a similar case because it's a new country and so I believe it's going to be extremely difficult, if not impossible, a new member state coming out of our countries getting the agreement of the others," he said.
The referendum in Scotland will be held Sept. 18, and voters will be asked whether Scotland should be an independent country, the BBC reported.
Scotland Finance Minister John Swinney said Barroso's comments were preposterous.
"He's set out his position linking and comparing Scotland to the situation in Kosovo. Scotland has been a member of the EU for 40 years--we're already part of the European Union," he said.
Swinney said there is no indication that a member state would veto Scotland's membership.