The argument about an independent Scotland's relationship with the EU might seem just a little premature, two years before a referendum that polls say will reject independence. Anyway, you might have thought relations with the rest of the UK would be the paramount issue, as the SNP proposes to keep the Queen and the pound but reject Trident and the Barnett formula.

However, in this curious constitutional phoney war, the unionists have been pursuing Alex Salmond relentlessly on the EU and this week believe they've demolished his claim that Scotland would automatically retain membership after independence.

The first minister has always insisted that Scotland, as a "succession state", would have automatic entry into the EU when independence comes. The argument is that Scotland has been a member for 20 years, has been subject to European legislation for 40 and therefore could not be treated as a wholly new country applying for membership.

Nonsense, say the unionists. Scotland's membership could not be assumed and any application would have to go to the end of the queue. Indeed, since all the member states would have to agree on Scottish entry, the terms might be highly unfavourable because countries like Spain and France fear the growth of separatist movements at home.

In September the president of the European commission, Jose Manuel Barroso, appeared to endorse the unionists case when he said that "a new state, if it wants to join the European Union, has to apply to become a member of the European Union just like any other state". This week, a draft letter from the commission to the House of Lords economic affairs committee, leaked to the Scotsman newspaper, added that "if a territory of a member state ceases to be part of that member state because it has become an independent state then the treaties would cease to apply to the territory".

It has since turned out that this has not actually been sent but that Barroso has indicated, in a letter to a Scottish MEP, that this is indeed his view. So it seems clear that Brussels is in no mood to wave an independent Scotland into the EU, no questions asked.

The SNP is furious about this. No one doubts that Scotland would fulfil the Copenhagen entry qualifications, as it is a democracy, fully signed up to the human rights convention and runs a free market economy. It is also one of the wealthiest areas of the union with its natural resources of hydrocarbon and green energy. Nor is there any actual mechanism for excluding a country that has been in the EU.

But the commission is anxious not to appear to be encouraging secession. The autonomous region of Catalonia in Spain has been seeking an independence referendum along Scottish lines. Madrid has argued that this is unconstitutional and is refusing Barcelona's right to hold one. This could mean that Catalonia, if it perseveres, would be a secessionist state and would be declared illegal in the eyes of the Spanish government – and, arguably in the eyes of the EU, though there is nothing in any of its treaties that says secession is illegal.

Salmond has responded by arguing that, as the Scottish referendum is legal under UK law and Westminster has agreed to accept the outcome under the Edinburgh agreement, then the EU could not refuse Scotland's entry – which would anyway be negotiated in the two years between the 2014 referendum and Scotland becoming formally independent in 2016.

Indeed, the SNP argues that both Scotland and the rest-of-the-UK would be in the same boat; if Scotland had to negotiate terms, so would the RUK. There would certainly have to be changes to the UK's contribution to the EU budget and its voting weight on the council of ministers should Britain lose a third of its land mass and most of its oil. The irony, of course, is that if Scotland becomes independent and seeks EU entry, it could well meet the UK going in the other direction.

If the Conservatives win the next election, a referendum on EU membership is looking inevitable. No one, not even unionists, believe that Scotland would be refused entry after negotiations have been completed. It is not even inconceivable, should the SNP win the 2014 referendum, that we could see Scotland negotiating its way in at the same moment the UK is negotiating its way out. This could be complicated.