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.

The 5.2cm (two inch) solid silver Declaration Pound dates from 1643, a year after the English Civil War broke out.
It was struck in Oxford, at a new mint created to launch an official currency under Royalist control.
The coin's owner, from Dorset, took it into a Dorchester auction house, unaware of its significance.
Timothy Medhurst, a coin specialist at Duke's Auctioneers, said: "The coin has been handed down through several generations to the current owner, who had no idea of its value.
"It is a coin which is rare to find and it will cause a stir in the coin collecting world."
Its owner does not know how long it has been in their family or where it originally came from.
The coin marks Charles I's attempts to regain his failing power from the Parliamentarians led by Oliver Cromwell.
A legend inscribed on the back of the coin in Latin reads: "Let God arise and let his enemies be scattered".
It is seen as a declaration of the king's power and his belief in absolute monarchy.
The coin will be auctioned at Duke's on 12 March.
According to the National Archives, £1 in 1640 would have been worth £85.80 in 2005.

Five windows, including door panels, were smashed at Strawletterdallon Orange hall, near Newtownstewart in an attack discovered on Wednesday night.
Police described it as a sectarian hate crime.
The Orange Order said more windows were smashed at about 19:00 GMT on Thursday. The same hall was damaged five years ago in an arson attack.
The damage to the hall discovered on Wednesday is thought to have been caused during the previous night.
Inspector David McIlwaine said that the damage was caused to the rear of the building.
An Orange Order spokesman described those responsible as "mindless thugs intent on causing community division."
He said: "This was an act of wanton vandalism with the clear intention to cause damage and destruction to Orange property.
"However, the culprits are actually harming the wider community and groups who use the hall as a social hub and meeting place."
The Orange Order said that last year nine halls were targeted.
Claims that an independent Scotland may not be able to join the EU were "unwise and inaccurate", a former senior European official has said.
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An "extremely rare" £1 coin is expected fetch up to £50,000 when it is auctioned off.
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An Orange hall in County Tyrone has been attacked for the second time in two days.