Alex Salmond is facing accusations of hiding the full legal reality behind the Scottish Government’s assurances that an independent Scotland would enjoy fast-tracked membership of the EU.

The SNP leader launched his administration’s White Paper on independence last month by claiming legal advice given to the UK Government earlier this year described as “realistic” a period of 18 months of entry negotiations between Edinburgh and Brussels.

Holyrood’s Deputy First Minister, Nicola Sturgeon, recently claimed a breakaway Scotland would have a “smooth and quick” transition to full EU membership.

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But both Mr Salmond and Ms Sturgeon failed to mention a subsequent legal “clarification” given to the Edinburgh government on the politically crucial issue of EU membership.

The advice, shown to The Independent, highlights “serious unresolved issues” and potential difficulties in the process.

Likely problem points include voting rights in both the European Council and Parliament, the validity of current UK opt-outs, the use of the euro and what was termed “further financial questions”.

Catherine Stihler, a Labour MEP who has campaigned for greater transparency over Scotland’s position on EU membership, said: “Alex Salmond has form saying one thing in public but knowing the opposite to be true. On this issue you can’t trust a word he has to say. The idea that everything will be all right on the night just because he says so isn’t credible.”

Expert opinion from James Crawford and Alan Boyle, professors of international law at Cambridge and Edinburgh universities respectively, was included in an analysis of what would happen to the UK if Scotland left the Union.

The document was presented to both Westminster and Holyrood in February this year. The “18 months” period regularly quoted by Mr Salmond is not contained in the February document. But both Mr Salmond and his deputy lean on a comment Professor Crawford gave to the BBC around the time of its publication, in which he described the “Scottish estimate” of 18 months for negotiations on membership of international organisations as “realistic”.

In the legal clarification that has been delivered after February, Scotland is described as different from the seven countries currently waiting to join the EU. The updated legal advice for the UK Government, seen by Mr Salmond’s legal team, warns no time limit can confidently be placed on any negotiation period. And that although 18 months is a “reasonable estimate”, because the EU has not faced a situation that can be compared with Scotland’s position, the time frame could be longer.

Another key issue in the legal guidance that will further weaken the nationalists’ guarantees on Scotland staying in the EU is the need for “an accession treaty to be ratified by members”. This is described as likely to “add time” to the negotiation process.

Spain’s Prime Minister, Mariano Rajoy, indicated the uncertainty of a unanimous backing by all EU member states when he told a summit last month that if Scotland left the EU it would have to re-apply as a new member. He said: “A region that would separate from a member state of the EU would remain outside the EU – and that should be known by the Scots and the rest of Europe’s citizens.”

The Independent contacted Mr Salmond’s office and described the potential delays outlined in the new legal clarification. There was no denial that it had received the legal re-evaluation. A spokesperson for the Scottish Government repeated what Mr Salmond said when he launched the White Paper on independence: “It is clear Scotland can negotiate the terms of independent membership of the EU from within the EU, in the 18-month period between a vote for independence and independence day itself in March 2016. That is a timescale described by the UK Government’s own legal adviser as ‘realistic’.”