Professor Kenneth Armstrong, a specialist in European law, said the First Minister's desired Article 48 route to membership would have to be managed by the UK Government as the existing member state.
But, he said, France and others could see any attempt to do this as "a Trojan horse"; that is, opening up the EU treaty to secure the radical changes David Cameron wants to the UK's membership ahead of his planned 2017 in-out referendum.
This could mean, Mr Armstrong argued, that the SNP Government, following a Yes vote, might have to go down the slower Article 49 route, the usual one for aspiring member states, which would not have to involve Whitehall but which could take several years to complete.
The French Government has made it clear it regards the Prime Minister's desire for treaty change before 2017 as "very, very unlikely" and, at yesterday's UK-France summit in Brize Norton near Oxford, Mr Hollande, when asked about his host's ambition, replied coolly: "For the time being, we feel revising it is not a priority."
Mr Armstrong, who is director of Cambridge University's Centre for European Legal Studies, said: "One interesting potential side-effect of the Cameron-Hollande summit is that if President Hollande is unwilling to open up the treaty to renegotiation, he and other EU member states may be particularly resistant to the UK Government seeking to initiate the treaty amendment process, ostensibly for Scottish membership of the EU, for fear that it will be a Trojan horse."
He added: "That may yet force the Scottish Government down the Article 49 accession route. This shows the political risks inherent in the Scottish Government's EU strategy."
Mr Armstrong stressed any opening of the treaty could raise member states' fears that this would "inevitably bleed into a wider revision".
He added: "Once you fire the starting gun of a treaty amendment, you can't guarantee that everyone wants to run in the same direction."
The Scottish Government believes that an independent Scotland could negotiate its "smooth" and "seamless" transition to full membership of the EU in the 18 months between a Yes vote this September and independence day as set for March 24, 2016.
This is because, as the White Paper, states, "Scotland joined the EU in 1973" and so Scots would be continuing members of the EU.
Edinburgh would, it argues, be able to negotiate from a "position of strength" as Scotland would still be part of the existing UK member state until independence day. So, 18 months is a "realistic" timescale.
The UK Government disagrees. Last month, Scottish Secretary Alistair Carmichael argued that the First Minister's preferred Article 48 route was a "dead-end" and urged the Scottish Government to "take its head out of the sand".
But last night, a spokesman for the First Minister said: "An independent Scotland will continue as an EU member. The only threat to Scotland's European future comes from Westminster's proposed in-out referendum.
"It is inconceivable," he added, "that the EU would seek to expel five million citizens simply because they have made a democratic decision to become an independent member state and there is no EU treaty provision allowing such a move - as confirmed by experts like Graham Avery and Sir Davi d Edward."
l David Cameron has threatened to use the Parliament Act to force through plans for a referendum on EU membership after legislation was effectively killed by peers. The Prime Minister blamed Labour and the Liberal Democrats for the failure of the EU (Referendum) Bill, and insisted Tories would try again.