Senior Nato officials have warned Alex Salmond's government that an independent Scotland would be barred from joining Nato if there were any disputes over the basing of nuclear weapons on the Clyde.

The Guardian can reveal that a small group of Scottish civil servants travelled to Nato HQ in Brussels last month to discuss Scotland's options for joining the alliance if Salmond wins next year's independence referendum. They argued that an independent Scotland should be given special treatment because it was already a significant part of an existing, founder member of Nato, the UK.

It is understood that Nato officials said it might be possible to allow Scotland to start fast-track talks – but in a blow to Salmond's anti-nuclear strategy, the Scottish delegation was also told that no new member would be allowed to join Nato if that state had unresolved military or territorial disputes with other countries.

Under article 10 of the Nato treaty, one assistant general secretary of Nato said at the meeting on 6 July, new applicants also have to show a history of stable defence policies and structures as a minimum entry requirement. Article 10 also implies that every Nato member accepts the alliance's nuclear first-strike policy.Official sources in Edinburgh and London confirm that these issues were seen as coded warnings that the Scottish government's determination to close down the Trident nuclear submarine base at Faslane on the Clyde would be a major obstacle to Scotland's application.

Lord Robertson, a former secretary general of Nato and a defence secretary in Tony Blair's government, said Romania, Hungary and Bulgaria were expected to resolve disputes over Transylvania and crossings over the Danube before starting their Nato membership process.

"You're not expected to import problems with your neighbours into Nato and that's a very clear warning signal," Robertson said. He said Faslane's continued operations were integral to Nato's strategic concept.

He said Salmond knew there was an unbridgeable contradiction between Salmond's desire to join Nato and his pledge to remove nuclear weapons from Scotland. "He's taking the Scottish people for fools by claiming that [the SNP] would want Scotland to be in Nato but laying down conditions that would make it impossible. It's a confidence trick both on their membership and the Scottish people."

Salmond has made closing down the nuclear facilities at Faslane a cornerstone of his independence campaign. In an appeal to leftwing voters, the first minister has promised to make that non-nuclear policy legally binding in a new written constitution after independence.

But becoming a full member of Nato is regarded as an essential part of Salmond's plans to persuade sceptical middle-ground voters that an independent Scotland would still remain part of mainstream and powerful international institutions.

The threat to close Faslane is one of the biggest obstacles facing a deal between the Scottish and UK governments over independence, because of its strategic significance and the immense cost of relocating the Trident fleet and its warheads to a new base in England or Wales.

Nato officials stressed that any decision on accepting new members would be political, requiring a unanimous decision by member states, adding to the pressure on Salmond over resolving any conflicts on defence policy with the UK.

Although an independent Scotland would be seen as a new state and required to apply as a new member, in principle it could be possible for the Scottish government in Edinburgh to start talks about joining Nato while those bilateral discussions were going on.

That would boost Salmond's case that it is in Nato's interests for Scotland to be a full member of the alliance, because of its strategic position in the north-east Atlantic and its oil reserves.

The Guardian revealed last month that Ministry of Defence officials were studying plans to force Scotland to designate Faslane and the nearby nuclear warhead base at Coulport as sovereign UK territory, provoking a furious reaction from nationalists and anti-nuclear campaigners.

During the lengthy meetings, Nato officials added that in the event of a yes vote, the UK and Scotland would have a large number of significant defence issues to resolve in the 18 months before independence day — set by Salmond as taking place in March 2016, and before Scotland applied to join Nato.

Professor Malcolm Chalmers, director of UK defence policy studies at the Royal United Services Institute think tank, who has analysed the Scottish government's defence strategy, said Trident's future would be of critical importance.

Chalmers said other Nato members would expect London to take the lead in settling the Trident issue and all other defence questions before they seriously entertained Scottish membership.

He said that pragmatists in the SNP accepted that would likely involve a long-term basing deal with the UK to keep Trident on the Clyde, but that would not be as dramatic as a sovereign basing agreement which would see Faslane declared to be UK territory.

Although Nato members would be keen for Scotland to join quickly and smoothly, "people would want Scotland to be a member but it would be in terms of not wanting any problems to be imported [into the alliance], but the main judge of the importing problems question would be London.

"I can't see a scenario with Scotland being a problem for Nato, provided it had sorted out any bilateral problems with England." He said no-one in Nato wanted to see Scotland being left outside the alliance.

• This article was amended on 15 August 2013. The earlier version said Alex Salmond had "made closing Faslane a cornerstone of his independence campaign", using "Faslane" as shorthand for the nuclear weapons facilities on the Clyde. The Scottish National party has asked us to clarify that it would continue to use Faslane as a naval base and a Scottish defence force headquarters after independence: it would close Faslane's nuclear facilities but not the entire base.