European Commission President Jose Manuel Barroso has said it would be "extremely difficult, if not impossible" for Scotland to join.
Jim Currie, a former European Commission director general, said Scotland had a right to membership.
Mr Currie was giving evidence to the Scottish Parliament Europe committee.
He also warned there could be tough negotiations on Scotland's share of the UK's EU opt-outs, in the event of a "Yes" vote in the 18 September referendum.
Mr Currie said: "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."
Mr Barosso has said he doubted Scotland could obtain the agreement of all of the EU's 28 members states, which would be a requirement for entry.
He previously told the BBC's Andrew Marr show: "We've seen that Spain has been opposing even the recognition of Kosovo, for instance, so it's 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 one of our countries getting the agreement of the other."
Commenting on Mr Barosso's words, Mr Currie said: "The statement he made was extremely unwise and I also think it was inaccurate."
He added that he thought "Kosovo was an unfortunate example" for the European Commission president to use.
Spain has seen a dramatic rise in support for Catalan independence in recent years, leading to speculation that Madrid could oppose Scotland's EU membership as it does not want to encourage the movement in Catalonia.
However, the Spanish government has not indicated that this would be the case.
Claims that an independent Scotland may not be able to join the EU were "unwise and inaccurate", a former senior European official has said.