THE UK defence secretary will be able to seize parts of the Crown Estate against the wishes of Scottish ministers even after control of the assets are transferred to Holyrood, it has emerged.

A draft memorandum of understanding, which sets out the terms of the new relationship between the UK and Scottish Governments following devolution in the area, gives the Ministry of Defence power to extend existing agreements with the Crown Estate and take over new parts of the land for defence purposes, even if the measures are opposed from Edinburgh.

Following last year's referendum, the Smith Commission recommended that management of the Crown Estate north of the border, which includes a large property portfolio, half the coastal foreshore and almost all the seabed, should be devolved.

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However, it also stated that an agreement should be drawn up between the administrations to ensure that transferring power was not "detrimental to UK-wide critical national infrastructure," such as defence capabilities.

The draft memorandum, which will be discussed this week by a Holyrood committee, makes clear that the UK defence secretary will retain significant power over the Crown Estate in Scotland, with waters used extensively by Trident submarines.

Under the deal, he or she will be able to extend existing agreements between the Crown Estate and the MoD, force through new agreements or even override existing deals with third parties if the UK Government decides that there is an "overriding public interest" in doing so for reasons of defence or national security.

The provisions in the draft memorandum have been included despite the UK Government already having powers to intervene if actions of the Scottish Government are seen as potentially harmful to defence interests.

Andy Wightman, a Green Party candidate at next May's Holyrood elections and land reform expert, said: "This complicated approach to Crown Estate devolution is unnecessarily convoluted, the draft order is riddled with inaccuracies and errors, and the Scotland Bill still fails to devolve the revenues of the Crown Estate. A process that could have been simple and straightforward has been hijacked by the Ministry of Defence and by an acquiescent Crown Estate Commission."

It is understood that the MoD was uncomfortable with transferring control of areas such as the Crown Estate and employment law to Holyrood, fearing Scottish ministers could use their powers creatively to interfere with its operations including the Trident nuclear deterrent. Crown Estate land in Scotland includes the base for the UK's entire submarine fleet, including its nuclear arsenal, and is also used for intelligence gathering and testing military hardware.

Documents released under Freedom of Information legislation revealed that during the Smith talks, the MoD requested that the term "anything which impacts on the operational effectiveness of conducting defence business should be excluded" be included in the final report.

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It also raised concern devolving health and safety law may lead to "different priorities, goals and potentially also different inspections" if regulation was controlled by Holyrood, which "could have implications for the delivery of defence outputs, including the nuclear deterrent."

Both the SNP and Scottish Labour oppose renewal of the nuclear deterrent, with three quarters of MSPs voting in favour of scrapping Trident in a recent vote.

A UK government spokesman said: "The Crown Estate transfer scheme will include protections for defence, supported by a complementary memorandum of understanding between the UK and Scottish Governments.

"The Crown Estate in Scotland is key to delivering strategic capabilities for the defence and security of the whole of the UK. These defence capabilities need to be protected to secure future use of the Crown Estate in Scotland, given the unpredictable nature of future threats to the UK."