A top-secret £634 million project vital for renewing the Trident nuclear weapons system has been halted following design and management difficulties, according to the government's Office for Nuclear Regulation (ONR).

This could undermine the UK government's entire plan to replace Trident, say critics. They are demanding investigations by the National Audit Office and by the Ministry of Defence (MoD).

The MoD insisted that work towards replacing Trident was continuing, though it was being kept "under close review". Insiders, however, have claimed that key projects are faltering and could be cancelled.

Since 2013 the private consortium that runs the Atomic Weapons Establishment (AWE) for the MoD has been building a plant, codenamed Pegasus, to make enriched uranium components for nuclear warheads and fuel for nuclear submarines based on the Clyde.

But in response to a freedom of information request, ONR has revealed that Pegasus - named after a fabled flying horse - has been grounded. "AWE has placed the Pegasus project on-hold and is currently re-assessing requirements for project delivery", said ONR. A "revised scope and delivery schedule" was now awaited.

Internal documents released by ONR show that Pegasus had been "subject to a large number of changes from the start". There had been problems with "senior management churn", "poor engagement" and "email ping-pong" at AWE.

There had been a "reluctance of AWE staff to talk with ONR", according to the minute of a special meeting to discuss delays in 2013. Safety reports needed to be "of better quality", it said, and the regulatory process for Pegasus had started late and taken "longer than planned".

ONR also expressed specific concern about one issue, though its description has been blacked out so it's unclear what it was. "So much had to be taken on trust and any vagueness caused great difficulties with permissioning," it said.

The SNP's Westminster leader and defence spokesman Angus Robertson MP warned that the whole Trident replacement project was now in jeopardy. "The revelation that Pegasus has been halted must throw into doubt the UK Government's mad plan to renew the nuclear deterrent," he told the Sunday Herald.

"It is alarming that a massive project like Trident, the sole aim of which is ensuring the UK can start a nuclear Armageddon, is clearly out of control with virtually no oversight. We need clear answers about what is going on as the whole Trident programme is getting more and more swamped in difficulties."

The MoD had some serious questions to answer, Robertson argued. "It's clear that another £600 million here or there is of no concern to the UK government when it comes to weapons of mass destruction."

The former Liberal Democrat defence minister, Sir Nick Harvey MP, has asked the National Audit Office to investigate. "We do need some clarification into the status of Pegasus," he said.

"The necessity for value for money across all public projects combined with a lack of broader scrutiny in the nuclear sector means the need for proper audit is more important than ever."

Pegasus is meant to replace an ageing 60-year-old facility known as A45 at Aldermaston in Berkshire. It was closed down for repairs in 2012 following the discovery of corrosion in its steel frame.

Harvey pointed out that A45 had a limited life. "There are already some question marks over its operational sustainability. Any delays to the new facility will put further pressure on," he said.

The MoD's 2007 business case for building Pegasus, released under freedom of information law, described A45 as "incapable of meeting future capability and regulatory requirements". Safety regulators have said that A45 should be replaced by 2016.

An anonymous group of AWE staff, calling themselves 'The Concerned Taxpayers', suggested in 2014 that Pegasus would have problems handling plutonium-contaminated enriched uranium. It was a "white elephant" that would be abandoned, they claimed.

It was "fantasy land" to suggest that Pegasus would be completed in the next few years and this was "due to incompetence", they said. "Pegasus will be closed down, A45 will undergo extensive refurbishment to prolong its ability to function and then it will be back to the drawing board."

AWE, which brings together two US companies, Lockheed Martin and Jacobs, with the UK company, Serco, declined to comment. Critics suspect that AWE is running into problems with another top-secret £724 million nuclear weapons plant called Mensa being built at Burghfield, near Aldermaston.

The Concerned Taxpayers have alleged that Mensa has gone hugely over budget and has been delayed by years, creating "a truly shambolic situation". The plant is designed to replace facilities from the 1960s known as gravel gerties where warheads are taken apart and put together.

The MoD, however, stressed that work on the capability for replacing Trident had not stopped. "Work is continuing on projects Mensa and Pegasus, which are part of the wider Nuclear Warhead Capability Sustainment Programme at AWE," said an MoD spokeswoman.

"All elements of this programme are routinely kept under close review to ensure they meet the MoD's requirements."

But Peter Burt from the Nuclear Information Service in Reading, which obtained the documents from ONR, described the problems at AWE as "a significant setback" to the Trident programme. "They will result in increased costs to the public and add to safety risks," he warned.

He also accused AWE of pocketing huge profits but failing to deliver. "It is running rings round the MoD and safety regulators, who are powerless to bring about improvements in standards," he said.

"All the evidence shows that AWE are struggling to meet the terms of their contract. It's time for the MoD to review its deal with AWE, fine the company for its poor performance, and if necessary suspend the contract and bring in a more competent management team."