The MoD is looking for somewhere to store radioactive components until the 2040s when a permanent disposal facility is due to be ready.
The shortlisted sites are Capenhurst, Cheshire; Sellafield, West Cumbria; Aldermaston and Burghfield, Berkshire; and Chapelcross, Dumfriesshire.
The components are from 18 redundant submarines and nine still in service.
The redundant Royal Navy submarines are currently stored afloat at Devonport, Plymouth; and Rosyth, Fife; but cannot be dismantled until the reactor components have been removed.
'Safe and sustainable'
After the site is chosen, the radioactive parts will be stored until after 2040, when the UK's Geological Disposal Facility, for the permanent disposal of spent fuel and nuclear waste, is planned to come into operation.
No decision will be made until after a public consultation later this year.
Of the shortlisted sites, the Atomic Weapons Establishment sites at Aldermaston and Burghfield are owned by the MoD and run by AWE Plc; Sellafield and Chapelcross are owned by the Nuclear Decommissioning Authority (NDA); and Capenhurst is run by Capenhurst Nuclear Services.
Philip Dunne, minister for defence equipment support and technology, said: “This is another step towards a safe and sustainable solution for the disposal of radioactive waste from our submarine fleet.
“All of the potential sites have a proven track record in handling radioactive material in a safe and secure way.”
The dismantling work will take place at Devonport and Rosyth.