Lenders based north of the border were responsible for over a quarter of all mortgages completed in 2011-12, according to a government report. Of the loans made by Scottish lenders, 84% or 204,645 loans were secured on properties outside of Scotland.

Edinburgh-based RBS was the fifth largest UK mortgage lender of 2011, advancing £14.6bn in new gross mortgage lending according to Council of Mortgage Lenders data. Lloyds Banking Group, which includes Edinburgh-based HBOS, was first with £28bn in lending. Clydesdale was eleventh.

The report argued independence would make it more difficult for lenders: “A key risk of independence is that the Scottish banking sector would likely be perceived as more vulnerable, resulting in higher funding costs which are then passed on to consumers”

The examples of the Republic of Ireland and the European Union suggested selling mortgages across borders was rare, it added.

Scottish lenders could struggle to raise funds via deposits because there would be less confidence among savers about an independent government’s ability to guarantee deposits in a future crisis, the paper suggested. Lenders’ wholesale market funding might also suffer without the trusted ‘UK’ brand keeping costs down.

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A Council of Mortgage Lenders spokesman said the lenders’ body was studying the report and would respond fully in due course: “It is clear, however, that Scottish independence could have far-reaching consequences for the mortgage industry, and could add to costs and complexity for firms and consumers.”

Should Scotland become independent, its financial services industry would also be subject to independent regulation. At present, Scottish financial firms contribute a fifth of industry funding of regulators.

The Scottish National Party-led Scottish government’s Fiscal Commission Working Group has suggested Scottish prudential regulation would be consistent with that in England, Scotland and Wales. However, conduct regulation would be subject to a different set of standards.

A pro-union Better Together spokesman said everyone in the UK benefited from being part of a single market: “There is one regulatory system and it makes no difference to mortgage providers where they are based or where their customers are based. The nationalists want to put a border in the middle of this single market. This would mean more and different regulation.

“This will mean that where companies and customers are based within the UK all of a sudden does matter. This cannot be good for business. It cannot make things easier, more efficient or cheaper than they are now.”

The pro-independence Yes Scotland campaign described the report as a “hasty rewrite” after the loss of the UK’s AAA credit rating led it to drop references to it in the report.

A spokesman said mortgage lenders should look at the recommendations of the Fiscal Commission Working Group: “This group consists of five highly respected international economists, including two Nobel Laureates. They have set out very clearly how we can use a shared currency and continue a single market for financial services.

“This will mean that mortgage lenders based in Scotland will continue to have the same opportunities as today. As the Scottish Secretary, Michael Moore MP, has said, Scotland can continue to use the pound and similarly No campaign leader, Alistair Darling MP has said an independent Scotland should continue to use it.”