As many as five of the sites under consideration – for storing up to 500 cubic metres of toxic scrap from 27 submarines – are in Scotland. They are the two naval nuclear bases on the Clyde, at Coulport and Faslane, the Rosyth dockyard in Fife, the Dounreay nuclear plant in Caithness and possibly the Hunterston nuclear power station in North Ayrshire.

Confidential documents leaked from the government’s Nuclear Decommissioning Authority (NDA) disclose official fears that such stores are like to be regarded as “contentious” because of the “sensitivity of military waste being ‘dumped’ on other communities”.

MPs and MSPs representing the targeted areas have warned they will fight any plans for turning their regions into nuclear waste dumps, and the MoD has been accused of “secrecy and spin”.

Since Britain launched its first nuclear-powered submarine, HMS Dreadnought, in 1960, 15 of the vessels have been taken out of service and defuelled. Seven are now moored at Rosyth, with the remaining eight at the Devonport naval base in Plymouth.

But storage space at the dockyards is limited, and a further 12 nuclear submarines still in service are due to be retired before 2040. Each sub has a ­reactor compartment, about the size of two double-decker buses, which is contaminated with radioactivity.

Since 1998, the MoD has been trying to find ways of breaking up the submarines and storing their radioactive waste for decades prior to disposal in a deep underground repository.

Now it has drawn up a “provisional list of sites” for dismantling and then storing the waste, but it refuses to identify them. However, the two sites it has earmarked for dismantling are assumed to be Rosyth and Devonport.

The locations of the additional 12 possible storage sites have been disclosed by leaked documents and other evidence uncovered by the Sunday Herald.

A report from the NDA, dated September 10 and marked “restricted”, concludes that seven sites where civil nuclear facilities are being decommissioned are “technically credible”, including Dounreay and Hunterston A.

The MoD has since told stakeholders only five NDA sites are now on its shortlist, but it is unclear which two have been dropped. The MoD is also looking at seven other military sites as potential waste stores. As well as Coulport, Faslane and Rosyth in Scotland, they include two locations at Devonport, as well as the Aldermaston and Burghfield nuclear weapons plants in Berkshire.

The leaked report warns: “Gaining planning consent for the storage of third-party waste packages within an NDA waste store is likely to be regarded as contentious by local authorities and communities. Obtaining suitable planning consents cannot be guaranteed.”

Another leaked NDA document highlights a list of “potential stakeholder concerns” about the proposed waste stores. They include “safety and security both during transport and storage”.

The MoD has written to the Liberal Democrat MPs for Fife and Argyll and Bute, Willie Rennie and Alan Reid, saying that one or more of the candidate sites were “within your locality”. But it did not say specifically where.

“We don’t want to be left with this nuclear mess,” said Mr Rennie. “It’s a blight on the area.” And Mr Reid promised to “vigorously oppose any future proposals to use sites in Argyll and Bute for breaking up nuclear submarines or dumping the nuclear waste”.

The NDA stressed that it was under “no obligation” to accept any submarine waste for storage. “No sites have so far been identified by the MoD as a credible option for such storage,” insisted an NDA spokesman.

The MoD said that the 12 potential storage sites will be subject to a strategic environmental assessment and then put out for public consultation. “It would be inappropriate to release details of these sites at this time,” said an MoD spokesman.

Jane Tallents, who represents non-government organisations on the advisory group of the submarine dismantling project, said that the MoD had been warned that keeping their shortlist secret would create speculation and alarm.

“Allowing information to get out in this haphazard fashion will only add to people’s suspicions that this is really all being decided behind closed doors,” she said.