Westminster warnings that the bill for ridding an independent Scotland of Trident would run into billions have been undermined by revelations that the UK Government previously put the cost at £150 million.

Warnings about the cost of getting rid of the missiles – a major plank of the SNP's plans in the wake of a Yes vote in the 2014 referendum – were voiced by UK Defence Secretary Philip Hammond, who last week told the House of Commons Defence Select Committee: "It would cost a significant amount of money."

Quotes from Ministry of Defence sources in a Guardian report claimed the department was looking at ways of designating Faslane as sovereign UK territory if Scotland votes for independence.

A source said: "It would cost a huge amount of money, running into tens of billions of pounds, to decommission Faslane. Those costs would be factored into any negotiations on an independence settlement. The sovereign base area is an option. It is an interesting idea because the costs of moving out of Faslane are eye-wateringly high."

But the Sunday Herald can reveal that the cost of dismantling all the UK's nuclear warheads was officially estimated as being significantly lower – less than £150m – by the MoD in 2006, in answer to an MP asking for a breakdown of the nuclear decommissioning costs.

Westminster could argue that the "tens of billions" figure does not involve dismantling the warheads but rather the decommissioning of Faslane and the costs of rehousing the submarines outside Scotland. However, it is far from clear why the Scottish Government would be expected to pick up any of those costs. Getting rid of Trident can be achieved by the far cheaper option of simply dismantling the weapons.

The difference between the costs has been seized on by the Scottish Campaign for Nuclear Disarmament (SCND), which last year published a four-year timetable for dismantling Trident, endorsed by the Scottish Government and experts.

"Scrapping Trident would be far cheaper than building a new base in England, even if, as is unlikely, the MoD found a suitable site," said SCND co-ordinator John Ainslie.

"Removing and dismantling the current stockpile of about 200 nuclear warheads would cost less than £150m. In contrast, a new Trident base would cost billions and a replacement for Trident would cost £100 billion over 50 years."

The warheads could be disabled within one year, removed from Scotland within two and dismantled within four. "Scrapping Trident is not just the right moral choice, it is the cheapest option," argued Ainslie.

In May, former UN weapons inspector Hans Blix urged the UK to give up Trident, questioning whether the nuclear system was "to protect UK independence or UK pride".

The SNP Westminster leader and defence spokesman, Angus Robertson, welcomed the low cost of dismantling Trident: "These figures underline that the UK Government would do well to follow the advice of Hans Blix and scrap Trident altogether, rather than waste money dumping it anywhere else."

Robertson has demanded an inquiry into the report of the plans to annex the nuclear bases on the Clyde if Scotland opts for independence.

He has written to Philip Hammond calling for a full investigation into the MoD's involvement with "this crazy and offensive idea".

Robertson is demanding to know "who commissioned this work, whether any Government minister approved it, which ministers were aware of it and when". He is also asking for the findings of the investigation to be made public.

"The people of Scotland are entitled to know where this idea came from," he said. "Westminster annexing Faslane can only have been considered an option if work had been conducted within the MoD into this scenario, and other scenarios that we don't yet know about."

He added: "Instead of dreaming up such ridiculous ideas in secret, the UK Government should be sitting down with the Scottish Government to discuss the range of issues that will be require to be negotiated if we achieve a Yes vote next year."

Robertson wants to remove the nuclear weapons from Scotland "as soon as possible" after independence, but keep Faslane as a conventional naval base.

Before last week's report, the MoD had insisted it was not assessing post-independence scenarios because Scotland was bound to vote against independence.

The new suggestion was soon knocked on the head by Downing Street: "It's not a credible or sensible idea," insisted a spokesman, who dismissed annexation as a "non-starter". However, Westminster would face a major problem with Trident in the event of a Yes vote.

Moving the system, its support facilities and the base for the four Vanguard-class submarines that carry it, would be hugely expensive and may be practically impossible.

There are no firm estimates for the costs of relocation. All the English sites mooted – Devonport, Falmouth, Portland, Milford Haven and Barrow – are fraught with practical difficulties. Shifting Trident to any of them would involve massive disruption to communities and businesses.

So when the suggestion of keeping the Clyde bases as part of the UK surfaced last week, experts thought it was credible. Downing Street's swift dismissal of the idea was attributed to the desire to deprive the SNP of a propaganda gift in the war of words over the referendum.

Even if, post-referendum, Westminster was to annex the bases, that may not end the problem. Fred Dawson, a former senior MoD safety official, said the warheads would still have to be regularly transported through Scotland to be serviced at the nuclear bomb factories at Aldermaston and Burghfield in Berkshire.