The analysis, marked "restricted", points to 11 "potentially significant risks" at bomb-making sites and ports housing nuclear submarines, documents seen by the Guardian show.
They warn that efforts to reduce radioactive risks have been "weak", safety analyses "inconsistent" and attempts to cope with change "poor". Formal regulatory action has been taken at two naval dockyards: Devonport in Plymouth and Barrow-in-Furness in Cumbria.
The reports also reveal that there is "no funded plan" for the decommissioning of Britain's 16 defunct nuclear submarines. Nine are moored at Devonport and seven at Rosyth on the Firth of Forth.
The reports cover 2006 and 2007 and were written by Rear Admiral Nigel Guild, chairman of the defence nuclear environment and safety board, an agency within the MoD that oversees nuclear safety. They were released in response to requests under the Freedom of Information Act 2000.
Guild identified 11 "potentially significant risks" at sites across the UK, including the atomic bomb factories at Aldermaston and Burghfield in Berkshire and the nuclear submarine and weapons bases on the Clyde near Glasgow. The workforce, the public and the environment were all being put at risk, he warned.
A 10% shortage of suitably qualified staff was "one of the greatest challenges to the sustainable future of the defence nuclear programme", he said - and it was getting worse. The MoD had to recruit “several hundred staff” over the next ten years, five times the usual recruitment rate.
Even before the spending squeeze on Whitehall under the coalition government, cuts in funding were hampering the MoD's ability to ensure good safety performance, according to the documents. "Often, in government, the management approach is to first impose a reduction in resource, and only then to assess its implications," Guild stated.
Fulfilling the legal requirement to reduce radiation exposure to "as low as reasonably practical" was often weakened by "excessive" cost estimates and delays, he said. Analyses meant to ensure the safety of weapons plants and submarine reactors were “inconsistent”.
Guild described the MoD's response to major organisational changes as "generally poor and significantly below best practice in the civil nuclear programmes". In 2007 he judged the risks posed by the MoD's lapses to be "degrading".
The control of potentially hazardous activities was also said to be "below best practice" at several sites, with particular problems highlighted at Devonport in 2006. Arrangements for the transport of warheads and other nuclear materials were "inconsistent" and emergency plans "have not accorded with standard UK practice".
Guild stressed that none of the risks were "an immediate safety or environmental concern". But there had been failures to comply with safety procedures.
"Without this compliance it will be increasingly difficult to continue to substantiate that the nucelar defence programmes are being managed with due regard for the protection of the workforce, the public and the environment," he said.
According to one former MoD official, nuclear safety had been compromised. Fred Dawson, who worked for the MoD for 31 years and was head of its radiation protection policy team before he retired in 2009, described the absence of funds for decommissioning nuclear submarines as "particularly damning".
He said: "It suggests that the need to make cost savings is being put ahead of the need to meet regulatory safety and environmental standards."
A spokeswoman for the MoD said that it took its safety responsibilities extremely seriously. Guild's role was to provide "assurance on safety and environmental aspects of the defence nuclear programme through a process of regulation and assessment," she said.
"This rightly involves the identification of areas requiring attention, with the objective of achieving ongoing improvement in safety performance to ensure that the UK's defence nuclear programmes continue to operate in a safe manner."
The MoD reports are available here.
An earlier story about MoD regulatory reports from 2005 and 2006 is here.