Trident nuclear submarines could remain on the Clyde for decades after Scottish independence, a top military analyst has warned.

An independent Scotland would also have to keep the UK's nuclear deterrent if it wanted to be part of Nato, according to Professor Malcolm Chalmers.

The defence policy director of the Royal United Services Institute (RUSI) also warns that independence would have a drastic effect on Scotland's defence industry. He describes the SNP's claims that Scotland would have armed forces to rival those of countries like Norway as "over optimistic".

The report is the latest in a series of warnings from military analysts. Last night Labour described the report as "devastating", but the SNP hit back as the report only allocated a £2 billion a year spend despite the fact that Scotland contributes £3.3bn annually to the UK's defences.

On Trident, the paper warns that recent historical precedents of countries becoming independent "suggest that [nuclear weapons] could remain for some considerable period of time, likely to be measured in decades rather than years".

Mr Chalmers also warned the defence budget would be "significantly less than those of neighbours such as Denmark and Norway", countries frequently cited by the SNP.

He warned that "much of Scotland's defence industry could, over time, migrate southwards in order to service the much larger UK market", and that a decision to withdraw from NATO would impact negatively on foreign relations.

Jim Murphy, the Labour shadow defence secretary, said: "This is a devastating, game-changing report that ends once and for all any idea that independence would be good for Scotland's defence."

Scottish Tory leader Ruth Davidson said: "The First Minister can't have his cake and eat it. Either he chooses to uphold his long-standing aim to get rid of nuclear weapons at Faslane – home to 6500 workers – and rip us out of the most successful military alliance in the globe or he backtracks on leaving Nato, which he has hinted he will do, and keeps the nuclear fleet."

Angus Robertson, the SNP's defence spokesperson, said: "An independent Scotland will not have unwanted, unneeded and hugely expensive Trident nuclear weapons based in Scottish waters, which will be removed in the soonest possible timescale – just as the vast majority of countries which co-operate on defence are also free of nuclear weapons, including Partnership for Peace members such as Sweden, Austria and Finland, and of course Norway, which is in NATO."