It fears the SNP could jeopardise the UK's nuclear weapons programme.
In an internal report summarising the main risks to Westminster's plans to keep submarine-launched, nuclear-tipped Trident missiles on the Clyde, the MoD describes the SNP's anti-nuclear stance as a "potential threat".
However, the SNP government has reiterated its promise to get rid of Trident through independence, and anti-nuclear groups say its future is now in the balance.
The SNP's long-standing policy, backed by the Scottish Parliament, has been to remove the missiles from the Clyde. Launching the Yes campaign for the independence referendum last month, the SNP leader and First Minister, Alex Salmond, promised to defend Scotland "without the obscenity of nuclear weapons".
The MoD has not previously admitted to taking the SNP's opposition seriously, but an internal "risk register" drawn up by senior officials points out that the MoD will need to comply with Scottish planning law when renewing the facilities at Faslane.
"The SNP have suggested they will exploit environmental legislation against basing Trident in Scotland," summarises the MoD report. "Potential threat to continued deterrent operations and support from Faslane/Coulport."
In order to "mitigate" this, the MoD says it will need "engagement of Scottish legal expertise to advise on issues and strategy". It also promises to "ensure continued ministerial and cross-Whitehall engagement on the political issue".
One example of such political engagement came last week, when UK defence ministers warned that Scotland might have to help meet the "gargantuan" costs of removing Trident. Nick Harvey, the Liberal Democrat armed forces minister, suggested that Faslane could become an English military stronghold in Scotland, similar to the US's Guantanamo Bay naval base in Cuba.
The MoD released its comments on the SNP last week because it was ordered to do so by the UK Information Commissioner, Christopher Graham, after an appeal by anti-nuclear campaigners. The risk register is dated October 2009, but is believed to still be current.
Peter Burt of the Nuclear Information Service, which obtained the register, argued that it was "far from guaranteed" Trident would be replaced. "The MoD is clearly concerned about the costs of the programme and worried its contractors won't be able to deliver new submarines," he said. "Ministers in London have been talking to their lawyers and planning to soft-soap Scotland's political leaders to prevent the Scottish government from scuppering Trident."
An independent Scotland would be the "death knell" for Trident, Burt maintained. But even if Scotland didn't vote for independence, it could still stymie the nuclear programme.
"Devo-max and even the current devolved arrangements could allow the government plenty of opportunity to ruin London's ambitions for developing nuclear weapons," he said.
The Scottish Government stressed that independence is the best way to get rid of Trident. "While the Scottish Government and devolved parliament are strongly opposed," said a spokesman, "independence is the only constitutional option which gives Scotland the powers to have Trident removed from Scottish waters."
The MoD reiterated that the UK Government is committed to maintaining a submarine-based nuclear deterrent. "There are no plans to move the deterrent from HM Naval Base Clyde," said a spokesman.
"The Defence Nuclear Executive Board's risk register identifies any potential issue that may have implications for the UK's nuclear deterrent and it is only right the MoD considers what mitigations might be appropriate."
A UK Government spokesman said: "For national security reasons, we need to understand all the issues around defence in the event of independence, including all policy options and their legality.
"However, we believe that the nations of our country are stronger together and that the majority of Scots believe this too. We don't anticipate that separation will take place."