Vital work at Britain's nuclear bomb factory has been halted for months because of safety fears, preventing Trident warheads from being shipped to and from the Clyde.

The ban on crucial maintenance at the Burghfield plant in Berkshire is believed to be the first time the Ministry of Defence (MoD) has ever been obliged to stop working on nuclear weapons. The implications, say critics, are "far-reaching".

Managers of ageing bomb dismantling facilities have been struggling for the last six years to remedy more than 1000 safety flaws uncovered by the government's Nuclear Installations Inspectorate (NII). But deadlines have been repeatedly broken.

Now the Atomic Weapons Establishment (AWE), which runs Burghfield, has been forced to cease "live nuclear work" while outstanding safety problems are fixed. The stoppage has been in place since at least December, though it was only admitted by AWE last week.

Burghfield is home to some of the most dangerous and secretive plants in the business of maintaining the Trident nuclear weapons system.

They are known as "Gravel Gerties", after a character from the 1950s comics featuring the US detective, Dick Tracy.

In circular cells buried under several metres of gravel, technicians take apart old nuclear warheads and put them back together again to check they are still functional. Great care has to be taken not to accidentally detonate the conventional high explosives that are packed around the plutonium core.

In the event of an explosion, the roofs of Gravel Gerties are designed to collapse, enabling the gravel to pour in and prevent plutonium from being blasted into the air. But there has been concern in the US about the risk of plutonium leaking out if an explosion fails to lift the roof.

Documents released under freedom of information law last year revealed that the NII was concerned about 1,000 "shortfalls" with equipment and procedures at the Gravel Gerties. They included deficiencies in roofs, doors, glove boxes, hoists, fire dampers, gas cylinders, cables and valves.

AWE's progress in fixing these problems was regarded as "unacceptably slow" by inspectors. The shortfalls were originally due to be dealt with by April 2006, but the deadline was postponed to April 2007, and then again to September 27.

Before the September deadline, the NII allowed bombs to carry on being dismantled in the Gravel Gerties because the MoD insisted the work was "necessary in support of the UK strategic deterrent". But this has now been stopped.

An NII report on its regulation of AWE, covering October to December 2007 and posted online this month, discloses that some of the shortfalls have still not been dealt with. "AWE has agreed that no live nuclear work will be carried out until the necessary fixes are in place," it says.

The report also reveals that 59 inspections were made of facilities at Burghfield and its sister plant at nearby Aldermaston in the last quarter of last year. In only two instances were the facilities defined as "good", while 43 were said to be "adequate" and 14 "had potential improvements identified".

Neither AWE nor the MoD were willing to talk about the implications or the details of the stoppage at Burghfield. But observers say it is unprecedented, and could have knock-on effects at Coulport and Faslane - the Clyde naval bases where Trident warheads are stored and loaded onto submarines.

John Ainslie, the co-ordinator of the Scottish Campaign for Nuclear Disarmament, said: "This will delay the navy's plan to overhaul the weapons that are based at Faslane and Coulport.

"It illustrates that there is no safe way to assemble or store these weapons of mass destruction."

Di McDonald, from the Nuclear Information Service in Southampton, suggests that the 140 or so warheads at Coulport will have to stay there, with those from returning submarines stacking up. Priority should be given to dismantling old warheads rather than building new ones, she argues.

"The irony for those of us seeking a non-nuclear defence policy is that it is essential that safe facilities exist to decommission warheads. Perhaps now is the time to rethink the whole Trident replacement proposal and go for the far easier, safer and cheaper option of disarmament."

The NII points out it has not taken legal action to stop operations at Burghfield.

A spokeswoman for NII said: "AWE has itself identified a number of packages of remediation work and has agreed with NII that it would not carry out live operations in any building until the remediation work has been satisfactorily completed."

The NII has adopted a regulatory strategy that aims to give permission for work to take place only when the safety defects have been fixed.

"It has taken this stance to ensure that sufficient priority is attached to addressing each of the shortfalls," the spokeswoman added.

AWE says it is carrying out a programme of work agreed with the NII to fix the shortfalls.

A spokesman for the group said: "The company has informed the regulator that we will carry out no live nuclear work until the agreed work has been completed.

"At no time has the safety of operations at Burghfield been in question."