David Cameron, the Conservative leader, has provoked a turf war with Alex Salmond by warning him not get in the way of plans to deploy a new generation of nuclear submarines in Scottish waters.

Speaking on the eve of the tenth anniversary of the opening of the Scottish parliament, Cameron said the SNP government should keep out of Westminster affairs, including Britain’s nuclear deterrent.

His remarks are a departure from the Tory strategy of avoiding confrontation with the SNP to deny Salmond the opportunity to provoke arguments with Westminster.

The first minister is expected to use the nuclear issue to try to build support for Scottish independence ahead of his planned referendum next year.

Salmond is confident that a Tory victory at the general election would increase support for independence, given the party’s unpopularity in Scotland.

The nationalists regard Cameron’s latest comments as a gift, given that an ICM poll in 2007 found that 64% of Scots were against nuclear weapons in Scottish waters.

In Holyrood and the Search for Scotland’s Soul, to be broadcast on BBC One Scotland tonight , Cameron cautions Salmond against attempting to “obstruct” the deployment of a new generation of Trident submarines on the Clyde.

The Tory leader said he would “respect” the right of the SNP first minister and the Scottish parliament to govern on devolved issues such as education and the health service.

However, he said that Salmond had to accept that the prime minister had a mandate to govern the whole of the UK in reserved areas, including defence.

“Defence is a UK issue. My party supports Britain having a nuclear deterrent that is independent. This is important and that’s a mandate, if we’re elected, that we will have to deliver,” he said.

“If a government in Westminster has a mandate to deliver issues to do with nuclear deterrence or the size of the army or whatever then they should be able to do that without the Scottish government trying to obstruct them.”

The Ministry of Defence (MoD) announced in May that the Faslane naval base would become home to all of the vessels in the the Royal Navy’s nuclear-powered submarine fleet by 2017.

While Cameron would be able to reverse the decision as prime minister, his comments indicate that he would press ahead with the plan.

Faslane is home to four Vanguard-class submarines, which provide the UK’s nuclear deterrent.

Under the MoD plans, HMS Astute, and three other hunter-killer submarines in the same class that are yet to be built, which are replacements for the Trident nuclear deterrent will also be stationed at the Faslane base.

Salmond intends to use environmental powers available to Holyrood to prevent the regular shipment of Trident warheads and components by road north of the border.

Convoys of 10 or more vehicles travel the 500-mile route from the Atomic Weapons Establishment at Aldermaston, in Berkshire, to the Royal Naval Armaments Depot at Coulport, Argyllshire — where the warheads are fitted to missiles — up to six times a year.

Salmond said it was “perfectly legitimate for the parliament to try to exert these powers to influence what happens in Scotland”.

Asked whether he would “roll over” and accept the UK mandate on this issue, he said: “I am not a rolling-over sort of person. The idea that you can base a new generation of nuclear missiles in Scotland, and not talk or listen to the people of Scotland about it, is ridiculous.”

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