The Scottish National Party has insisted that an independent Scotland would not have to reapply for entry to the European Union.
John Swinney said Mr Prodi was incorrect
A statement from European Commission president Romano Prodi implied that any newly-independent region would have to make a fresh application to join.
But SNP leader John Swinney said Mr Prodi was not correct.
He said Scotland would automatically remain part of the European Union if it were to separate from Britain.
Mr Swinney said that a body of legal opinion over the past two decades backed up his view that an independent Scotland would remain part of the EU.
"I think we have to remember that Mr Prodi is not a dispassionate civil servant. Mr Prodi is an Italian politician wanting to become the next prime minister of Italy.
"I suspect he has got an eye on domestic politics when he has made the comments he has just made."
Mr Prodi gave his view when Welsh Labour MEP Eluned Morgan asked a general question about whether a newly-independent region would have to leave the EU and apply afresh for accession.
In a written answer that gave no examples and named no countries, he told her: "When a part of the territory of a member state ceases to be part of that
state, e.g. because that territory becomes an independent state, the treaties
will no longer apply to that territory.
Mr Prodi gave his view to a Welsh MEP
"In other words, a newly-independent region would, by the fact of its independence, become a third country with respect to the (European) Union and
the treaties would, from the day of its independence, not apply any more in its territory."
Mr Prodi went on to detail how any European state can apply to join the EU, and an application would require negotiations about an agreement about the
conditions of admission.
"This agreement is subject to ratification by all member states and the applicant state," said Mr Prodi.
Mr Swinney said the real question was not about "legal nitpicking" but about whether Scotland was going to be at the top tables of Europe.
He said: "On 1 May, 10 countries are going to be joining the EU - 10 new accession
states, some of them smaller than the city of Edinburgh.
"They are going to be joining the EU, sitting around the top table of Europe, having more say in the domestic and international issues affecting Scotland that
people in Scotland currently have."