Mark Neale, head of the Financial Services Compensation Scheme, the industry-funded safety net which guarantees up to £85,000 per saver, said EU law meant a separate Scotland could no longer be part of the UK mechanism.
"Were Scotland to become independent and were it join the EU, it would be required by European law to have its own deposit protection arrangement within its own jurisdiction," said Neale.
EU directives say member states "must be able to finance those arrangements", he added. The Scottish Government's economic advisers have suggested that Scotland could agree to share services after independence, consistent with European moves to "harmonise" schemes.
Neale said no approach had yet been made by Scottish ministers on that point.
An SNP spokeswoman said: "An independent Scotland will have a deposit guarantee scheme not just because it is sensible, but because it is a requirement of EU law, and the full range of financial products will continue to be available."