The report seeks to contrast the safety of the submarines' reactors with those used in the civil nuclear industry and concludes that they compare poorly.
In particular, it claims they are vulnerable to a structural failure, which could result in the release of highly radioactive material into the environment.
The document was released after the Campaign for Nuclear Disarmament requested it under the Freedom of Information Act.
Last night, the Ministry of Defence (MoD) confirmed it was genuine but sought to play down any fears of imminent danger.
The Royal Navy operates 11 submarines powered by Rolls-Royce reactors. They include six Trafalgar-class attack submarines and four Vanguard class, which carry Trident ballistic nuclear missiles. It has also launched HMS Astute, the first of seven Astute-class submarines, which will also carry Rolls-Royce reactors.
Rolls-Royce refused to comment on the report.
The declassified document was written in November 2009 about the status of plans to replace the Vanguard submarines – one option being to build vessels using the same reactor as used in the older ones.
At the bottom of the document is an assessment of the safety of those reactors by the MoD's senior nuclear safety regulator, Commodore Andrew McFarlane.
He wrote: "All pressurised water reactors are potentially vulnerable to a structural failure in the primary circuit, causing a rapid depressurisation and boiling-off of most of the cooling water. This results in failure of the fuel cladding and a release of highly radioactive fission products outside the reactor core."
"While the further containment provided by the submarine's pressure hull may contain the majority of this material inside the submarine, some leakage is likely to occur and, in any event, the radioactive 'shine' from the submarine poses a significant risk to life to those in close proximity."
The report goes on to say current designs of UK and global civil power plants have systems to negate the danger, but that the submarine reactors "compare poorly" with those standards.
An MoD spokesman said that, while there were differences between these military reactors and civil reactors, the submarines' reactors met all defence safety standards.
He also pointed out that the Royal Navy had a "very good" safety record in relation to its nuclear submarines.
He said: "The MoD takes nuclear safety very seriously. All of our nuclear reactors meet the strict safety standards set by the defence nuclear safety regulator and we continuously look for areas of improvement."
John Large is the consulting nuclear engineer who helped oversee the salvage of the stricken Russian submarine Kursk after it sank in August 2000. He said: "To my mind, it is the MoD who have bungled here. The present generation of submarine reactors the Royal Navy has is not sufficient."
"Rolls-Royce should be given the opportunity to correct, modify or upgrade these nuclear power plants as far as it can. Yet, there is no provision for this work to be carried out in this document."
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