New European Commission President was plunged into instant controversy last week when his comments on putting the brake on new Eastern European entrants were seized on as an example of Scotland's fate.
But his office then made the specific point that he was not speaking about Scotland and it was claimed at the weekend that the former Prime Minister of Luxembourg would be "sympathetic" to Scottish entry, given that it is already signed up to "core EU requirements".
The BBC first reported that Mr Juncker's aides had rejected the suggestion he was referring to Scotland in his call for "consolidation" of the EU at a time of eastern advancement.
Yesterday it claimed that it had been told by a "high-ranking EU official" that Mr Juncker "would not want Scotland to be kept out" as it already met all of the criteria for membership.
It quoted the official as saying: Mr Juncker "would be sympathetic as someone who is from a smaller country as he'll understand the obstacles that can be put in the way of less powerful member states."
The official was also quoted as saying an independent Scotland would be treated as a different case to other candidates for EU membership, such as Albania, Iceland, Montenegro, Serbia, Turkey and Macedonia.
A spokesperson for First Minister Alex Salmond said: "This confirms what we've said all along. Scotland is already part of the EU and already meets all the requirements for membership.
"The specific terms of continued membership as an independent country will be negotiated in the 18-month transition timetable we have indicated - a timescale described as 'realistic' by the UK government's own legal adviser."
He added: "This proves that the No campaign's claims last week that Scotland would be out of the EU and have to get back in was yet more scaremongering from a clearly rattled No camp and Alistair Darling should apologise for misleading the Scottish public.
"An independent Scotland, as an equal member state, will bring a positive, co-operative voice to the EU.
"The only threat to Scotland's continued membership of the EU, with all the implications that would have for jobs and investment, is Westminster's proposed in-out referendum."
SNP Westminster leader Angus Robertson said: "This welcome report confirms what we already knew - as a current member of the EU, Scotland will be treated as a 'separate and special case', and will negotiate our member state status from within.
"The No campaign's credibility is in tatters as their scares on Europe are laid bare. Just days ago they were caught trying to twist Mr Juncker's words - which led to his spokesperson stepping in to make clear his comments were not about Scotland."