Papers released by the Public Records Office show the safety rating for Devonport Dockyard in Plymouth was substantially worse than those of Rosyth, Chatham and Belfast.
On 1 October 1964, the Nuclear Powered Warships Safety Committee said it "could not recommend Devonport as an acceptable site for a refitting yard for nuclear submarines".
But another report said a nuclear accident was near-impossible and would be "a major disaster" in any of the dockyards considered.
Portsmouth, Barrow and Birkenhead were also ruled out by Sir Solly Zuckerman's committee to consider sites for nuclear refits.
In July 1965, the Director General of Dockyards and Warships said the committee's recommendation made "any sensible planning" impossible.
Calculations were "so imprecise that there seems to be plenty of scope for a reassessment", he said.
"There is no need to stress how damaging to future developments the present recommendation is.
"It should be a great pity if current and transitory ideas on safety should force us into some other expedient."
Political decision
He recommended "a more subtle approach to the problem".
The same year, P T Heath, chairman of the Naval Nuclear Technical Safety Panel, wrote: "If refitting is to be carried out at these dockyards it can only be on the basis that there is not going to be an accident."
He added: "A decision of this nature would be political rather than technical."
At one stage, officials contemplated refitting submarines at Devonport in a covered dry dock, built to contain any nuclear leak.
But the idea was turned down because it would be too difficult to maintain equipment such as door seals and ventilation valves.
Safety ratings were based on the size of the population close to the dockyards.
Major disaster
They showed a release of 5-10 curies of radiation at Devonport would exceed exposure limits for children, compared with 200 at Rosyth in Scotland.
But one of the released sets of minutes - headed Secret - says that in either case, the figure was "completely swamped by the amount that would in all probability be released in the event of an accident".
"No matter where the accident occurred, it would constitute a major disaster."
Another report said "nothing short of a large scale mutiny or armed intervention" would compromise safety controls if Devonport was chosen.
Devonport Dockyard is now the Royal Navy's main base for refitting nuclear submarines.
Rosyth Dockyard in Scotland has lost its share of the work.
Reactor fault
People in Plymouth and south east Cornwall are currently campaigning against plans to increase leaks of radioactive tritium from submarines at Devonport into the River Tamar.
Extremely tight controls are operated by engineers doing nuclear refits.
But last week it emerged that a failure to detect a fault in a reactor during a refit of HMS Torbay in Devonport meant it would have to be stripped down and reassembled.