Nick Harvey, the Armed Forces Minister, told MPs on the Commons Scottish Affairs Committee that relocating the deterrent would be the Ministry of Defence's "least favourable option".
His comments came as a titanium-clad "egg" emerged as the launch venue for the cross-party campaign against independence, Better Together.
The futuristic 200-seat Lindsay Stewart building – looking out towards Edinburgh Castle from the Craiglockhart campus of Napier University – will host the event on Monday, June 25.
It will be led by former Labour chancellor Alistair Darling, backed by Annabel Goldie for the Scottish Conservatives and former Liberal Democrat leader Charles Kennedy.
Yesterday, Mr Harvey claimed that if an Edinburgh government could be persuaded to keep nuclear submarines on the Clyde, then the UK Government would seek to retain "complete control" over them.
Alan Reid, the Liberal Democrat MP for Argyll and Bute, asked what the UK Government's conditions would be should a Scottish Government agree to keep the nuclear deterrent.
Mr Harvey replied: "Complete freedom of action, complete control and complete sovereignty over the facility."
He told MPs the UK Government did not know the precise foreign or defence policy of the SNP should Scotland become independent as there had never been any detailed discussions with Holyrood, nor were there any contingency plans being drawn up by the MoD.
It follows comments in January by First Minister Alex Salmond that it was "inconceivable" an independent nation would tolerate nuclear weapons on its soil.
Mr Harvey explained that moving the nuclear facility from Faslane would be a "very challenging project, which would take a very long time to complete and cost a gargantuan sum of money".
He pointed out simply upgrading the Clyde facility cost £3.5 billion, and added: "If we were to replicate it somewhere else, that figure would be dwarfed."
He stressed that the impact of a future Scottish government demanding removal of the UK's nuclear deterrent would have a "very substantial" impact in post-independence talks.
He said: "It's hard to think of a single item that would be larger. Of all the issues that needed to be discussed that would stand out as one of the most difficult."
Labour backbencher Iain McKenzie suggested decommissioning would be included in the post-independence negotiations alongside the division of the national debt and the banking bail-out.
He said: "In the end, a compromise would be made as to who pays for what, so both sets of taxpayers would end up paying."
Meanwhile, more than 4000 people have volunteered to help the pro-independence cause since the launch of the Yes Scotland campaign by Mr Salmond less than three weeks ago.
A senior campaign source insisted: "It's a big figure. It works out at 76 people per constituency and that's just within three weeks.