Three-quarters of the incidents are blamed on human error, and are likely to include fires, leaks and procedural blunders. There have been "issues" with a system meant to protect an explosives store from lightning strikes, as well as problems caused by staff and resource shortages.
The MoD has also revealed it is planning a new conventional explosives handling facility at Coulport to deal with the extra nuclear submarines due to be based there over the next few years in the event of a No vote in the independence referendum.
The Scottish National Party's defence spokesman, Angus Robertson MP, called the revelations on safety "chilling", "shocking" and "simply unacceptable". However, the MoD said it was "entirely misleading" to focus on the number of reported incidents.
An MoD report on its annual review of safety at the Faslane nuclear submarine base and the Coulport nuclear bomb store in Argyll has been released under Freedom of Information law. Dated September 2012, it discloses how many "nuclear safety events" have occurred in recent years.
Between April 2008 and August 2012 there were 262 such events, most of which were attributed to "human factors". More than 50 incidents have been logged every year. The report does not describe any of the events, but MoD safety reports released for earlier years show that they can include radioactive contamination, small fires and failing to follow safety rules.
The figures do not include incidents involving nuclear weapons, for which no numbers are given. The report does say, however, that there have been "false alarms and system failures" with an "environmental hazard detection system" for the warheads.
The report also says "issues relating to the lightning protection system for the Faslane explosives store house have not yet been fully resolved". It makes a several references to other problems caused by shortages of staff and resources.
"Yet again safety at Faslane is an issue," said Robertson. "To have more than 50 nuclear safety events every year is simply unacceptable."
He described the MoD report as "shocking", and said that it was "chilling" to hear staff shortages and system failures mentioned in connection with nuclear weapons. "Nuclear safety has to be paramount at Faslane - and it is clearly not. That should be a matter of deep concern for everyone."
The Westminster Government's claim that Scotland's defence was safe in its hands was no longer credible, Robertson argued. "Trident is a hugely expensive weapon of mass destruction dumped on the Clyde, yet our regiments are cut to the bone and there are no ocean-going surface vessels based in Scotland."
John Ainslie, co-ordinator of the Scottish Campaign for Nuclear Disarmament, said there had been far too many safety incidents at Faslane and Coulport. "It is very worrying that the MoD is taking on additional nuclear work while they are short of key personnel," he said.
The MoD report revealed that the explosives handling jetty at Coulport will become overloaded as a new fleet of seven Astute-class submarines arrive on the Clyde. It said an "alternative ammunitioning capability" will be needed to take conventional torpedoes on and off the submarines. The MoD confirmed to the Sunday Herald that a new facility would be required. A spokesman said: "A currently unused jetty within RNAD Coulport, the MoD's existing dedicated weapons handling facility, will be reinstated to handle the ammunition."
The MoD spokesman added: "It is entirely misleading to focus only on the number of reports. Our comprehensive reporting system purposely captures even the most minor of incidents, which never pose a threat to the public or our personnel, to ensure all lessons are learned."