Joaquín Almunia – a fierce opponent of Catalan independence – said it would "not be honest" to say a breakaway region would be stuck outside the EU if it was independent.
Mr Almunia also insisted citizens of the EU could not be stripped of their rights just because their territory separated from a member state.
The vice-president, a member of Spain's opposition socialist party, was speaking before the country's Foreign Minister, José García-Margallo, on Tuesday cast doubts on Scotland's automatic re-entry in to the EU.
The Spanish Government faced immediate demands for a referendum from Catalonia after First Minister Alex Salmond and PM David Cameron signed the Edinburgh Agreement earlier this month.
Catalonia will hold a special general election next month with pro-independence parties expected to triumph.
Similar movements won regional elections in Spain's other potential breakaway region, Euskadi or the Basque country, this month. Both Catalan and Basque nationalists have cited the Edinburgh Agreement as they go the polls.
Mr Almunia, speaking in a previously unreported debate on Monday, said Mr Salmond and Mr Cameron had given Spain "a lesson in democracy".
Several prominent Spanish unionists have suggested the rhetoric coming from the Mariano Rajoy's government is counterproductive compared with Mr Cameron's willingness to accept a Scottish vote in 2014.
Mr Alumnia, however, fell well short of repeating claims from Spain that Catalunya or Scotland would have to remain outside the EU for a period.
He told a newspaper: "You cannot give a categorical answer that somebody who splits off would remain outside and we wouldn't know anything about them for centuries. It's not like that. If you are a European citizen you have certain rights."