The Clyde bases that host Britain's nuclear bombs and submarines are plagued by widespread safety flaws, according to an internal Ministry of Defence (MoD) report obtained by the Sunday Herald.

The SNP's defence spokesman in Westminster, Angus Robertson MP, said the problems at Faslane and Coulport "clearly put lives at risk" and demanded an urgent investigation.

The MoD's latest annual review of safety reveals that 11 of the bases' 13 activities have been officially declared unsatisfactory after assessments by site managers and regulators. The review was released last week in response to a request under freedom of information legislation.

Nine safety activities were colour-coded yellow because they were "below standard" and suffered "specific weaknesses". These included categories headed "weapons safety", "safety culture", "maintenance", "safety performance indicators", "site safety case", "nuclear safety event reporting" and "conventional health and safety including fire safety".

Two activities were coded orange because they were "significantly below standard" with "flawed" practices or procedures. They were headed "organisational change" and "operator experience feedback".

On nuclear weapons safety the review said there had been "shortfalls in specific areas or delays in progressing projects". No further details about the precise nature of the safety weaknesses were given in the review, or by the MoD.

The revelations were "of grave concern", according to the SNP's Robertson. "They point to serious systemic failures which could clearly put lives at risk," he said.

"The prospect of a major nuclear accident is unspeakable, with the potential to contaminate some of Scotland's most densely populated areas. The UK Government's nuclear inspectors must investigate this situation and examine whether current safeguards are adequate."

Robertson demanded "full disclosure" from the MoD on how the failures occurred and what it is doing to improve safety. "At a time when MoD policing at these bases is in question as a result of further UK government cuts, these safety failures will add to existing security concerns," he said.

Faslane, on Gareloch, is the home port for the four Vanguard-class submarines that carry Trident missiles, as well as other nuclear-powered submarines. Coulport, on Loch Long, is where nuclear warheads for the missiles are kept.

The Clyde safety review concluded that it was "properly representative of the site's safety performance."

Only two of the 13 subject areas were deemed "adequate" and coded green – "emergency arrangements" and "radiation safety and waste management". But on nuclear waste management the review disclosed a hitherto unknown problem.

A new plant for disposing of the radioactive waste created by submarine reactors was to have been in operation by 2014, when safety clearances for the old plant are due to run out. But now the new plant is not expected to come into service before 2017.

John Ainslie, the co-ordinator of the Scottish Campaign for Nuclear Disarmament, accused the MoD of moving the goalposts. "This old system will continue to leak radiation into the environment until 2017," he said. "The MoD should stop producing nuclear waste at Faslane if they have nowhere to put it."

The Scottish Environment Protection Agency (Sepa) confirmed that there was a "potential gap" in radioactive waste treatment facilities at Faslane. "To fill this gap MoD is proposing to extend the life of the existing radioactive effluent disposal facility and is carrying out works in support of this," said a Sepa spokeswoman.

The MoD insisted that it took safety very seriously. "The purpose of the annual review of safety is to identify areas for improvement in the naval base's safety management processes," said a MoD spokeswoman. "The review also makes clear that we are taking steps to remedy the issues raised."