Foreign Secretary William Hague said this week that if Scotland votes to leave the UK it will also leave the EU.
The Scottish Government says Scotland would negotiate a seamless transition into the EU in the 18 months between the referendum and its proposed independence day in 2016.
EC president Jose Manuel Barroso has said any new independent state would have to apply for EU membership.
David Grant Lawrence, a former EC director-general, said that anyone who claims to know for certain is "whistling in the wind".
Speaking at an event to mark the 40th anniversary of the UK's membership of the EU in Edinburgh, Mr Lawrence said it is "hard to envisage" Scots' EU citizenship being revoked.
"I was surprised by Mr Barroso's statement about Scotland's vote on independence," he said.
"It is clear to me that if Scotland votes for independence we would be in a situation where there would be no EU precedent."
On Tuesday, Mr Hague said that if Scotland left the UK, it would also leave the organisations the UK is a member of, including the EU.
But SNP MSP Christina McKelvie today accused Mr Hague of "playing politics" when his party has promised a referendum on the UK's continuing EU membership in 2016.