The UK's entire nuclear-powered submarine fleet will be told to leave the Clyde and go back to England if Scotland votes for independence in September, the Scottish Government has said.

This would deal a fatal blow to Ministry of Defence (MoD) plans to make the Faslane naval base near Helensburgh the UK home port for all its 14 reactor-driven submarines over the next few decades. As well as the four Trident submarines, three Trafalgar-class submarines and seven new Astute-class boats would all have to find a new base on the English coast.

The move has been warmly welcomed by anti-nuclear groups, who label the submarines "floating Chernobyls" after the devastating nuclear accident in Ukraine in 1986. But the MoD warned that ending Faslane's role as a submarine base "would seriously impair the UK's national security, including Scotland".

In 2011, the Scottish Government welcomed the decision to station Astute submarines at Faslane because of the jobs they would bring. But this was publicly opposed by prominent party activists, and has led to a change of heart.

The Scottish Government now says that it sees no role for any nuclear-powered submarines in an independent Scotland. "We do not see the continued basing of the Astute or Trafalgar fleets at Faslane, beyond the necessary transition period, to be in Scotland's interests," a spokeswoman told the Sunday Herald.

Scottish ministers expect the transition to take no longer than 10 years, suggesting that there would be no nuclear-powered submarines at Faslane by 2026. "The Scottish Government strongly favours a conventional approach to Scotland's defence, with Faslane being Scotland's main conventional naval base," the spokeswoman added.

"In the event of independence, it would be for the rest of the UK to decide whether to relocate its submarine fleet to the Royal Navy submarine base at HMNB Devonport or to another location."

Devonport, in Plymouth on the south coast of England, is the most likely alternative to Faslane. Trafalgar submarines are currently based there before their scheduled move to the Clyde by 2017.

The first two Astute submarines are already at Faslane, but the third, HMS Artful, has had its launch from Barrow in Cumbria delayed until later this year because of fears that an old dock there might collapse. The remaining four Astute boats are due to arrive at Faslane over the next 10 years.

The Scottish Campaign for Nuclear Disarmament argued that it would be relatively easy to relocate the submarines to Devonport. "We have lived for too long with these floating Chernobyls in our lochs," said campaign co-ordinator, John Ainslie.

"Independence offers the prospect of a completely nuclear-free Scotland, with no Trident, no nuclear power stations and no Astute submarines."

The MoD pointed out that the Clyde naval base was the biggest employment site in Scotland, with 6700 military and civilian jobs. This would rise to 8200 by 2022, as the nuclear-power submarines are all moved there, an MoD spokesman said. "We are not developing contingency plans as we are confident that the Scottish people will vote to remain part of the UK family," he argued. "Removing Faslane as an operating base for attack submarines would seriously impair the UK's national security, including Scotland."

But the Scottish Government said that it expected to maintain the number of military jobs at Faslane as it changed from a nuclear to a non-nuclear base. "Those military personnel will be supported by a significant number of civilian personnel," it said. "In addition, work to reconfigure Faslane as a conventional naval base is expected to involve major construction activity, and related jobs, in the area."