The Scottish Government has indicated for the first time that Scotland would not automatically be able to negotiate EU membership from within the organisation if Scots vote Yes in next year's referendum.

In a parliamentary answer yesterday, Deputy First Minister Nicola Sturgeon said she “expects” that to be the case but offered no firm guarantee.

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The SNP has previously insisted that, in the event of a Yes vote, Scotland would negotiate terms of EU membership during the transition period between the referendum and independence day in 2016.

It would mean Scotland negotiating with Brussels while it remained part of the UK and therefore in the EU.

But in a parliamentary answer to a question from Labour’s Ken Macintosh, Ms Sturgeon said she “expects Scotland’s transition from membership of the EU as part of the UK to membership as an independent member state to be negotiated from a position within the EU”.

The issue is crucial to the SNP’s “transition timetable”, published last week, as a rapid deal on EU membership would simplify independence negotiations with the rest of the UK.

Reciprocal arrangements  on a range of issues, including access to health care and  pension payments, already exist Europe-wide and would not  have to be negotiated separately by Holyrood and Westminster  if an independent Scotland  was a full EU member from moment it formally separated from Britain.

First Minister Alex Salmond and Blair Jenkins, the head of the pro-independence Yes Scotland campaign, have both recently insisted thatScotland would definitely negotiate with the EU “from within”.

However, they were challenged last week by Labour and Conservative MEPs, who claimed talks with Brussels could not start before Scotland became fully independent.

A Scottish Government spokesman said: “The position remains unchanged – ie, Scotland negotiating its continued membership of the EU as an independent country from within the EU.”

But Scottish Labour’s constitution spokeswoman Patricia Ferguson said: “This would appear to be the umpteenth SNP policy shift on Europe, and the result is even more uncertainty for Scots.

“Alex Salmond and Nicola Sturgeon have repeatedly asserted that Scotland would negotiate membership from within the EU without any evidence to base that on.

“Clearly, something has now happened behind the scenes which has forced them to admit this is far from certain.

“The more the SNP get caught misleading the public, the less likely they are to increase support for breaking up Britain. Scotland deserves an honest debate, and yet again the SNP has let the country down.”

Last year the Scottish Government abandoned its claim that an independent Scotland would enjoy automatic EU membership and inherit the same terms as the UK.

Ministers have since acknowledged the negotiations would be required on a range of key issues, including the eurosingle currency and Scotland’s share of Britain’s cash rebate. However, they say they would not join the euro.

The row came as Alistair Darling, head of the pro-UK Better Together campaign, suggested an independent  Scotland might have to wait years to become an EU member. He said Slovenia and Estonia – cited by the Scottish Government as examples of countries which gained independence quickly – took five and nine years respectively to join the EU.

The former chancellor said: “Even the examples the Nationalists quote in their own document show we would face a lengthy application process to the EU.”