A major row broke out after the BBC reported RBS plans to relocate the office to London, if there is a Yes vote, on Wednesday night. The bank's announcement was made the next morning.
It prompted First Minister Alex Salmond to write to Sir Jeremy Heywood, the head of the UK civil service, demanding an inquiry into the "clear breach of city rules".
In response, Heywood said the Treasury had just been confirming its understanding of RBS's plans after questions from the media.
But the Sunday Herald understands the Treasury sent an email to the BBC at 10.16pm on Wednesday, while the RBS board was still meeting to decide whether to tell its shareholders of its plan the next day.
The Sunday Herald understands the Treasury email said: "As you would expect, RBS have also been in touch with us and have similar plans to base themselves in London."
Salmond last night called the email ''an extraordinary and politically explosive revelation'' and demanded its immediate publication in full.
''It appears that the Treasury were briefing RBS market-sensitive information 45 minutes before the bank's board decided to announce its decision,'' he said.
''It is clear they did so in clear breach of the Treasury rule book. The Treasury fingerprints are all over this. They orchestrated it in the same way that the Prime Minister was caught red-handed orchestrating the scare surrounding comments by supermarkets.
''The Westminster establishment are now on the back foot. Not only are they fearmongering but they are not doing so competently or within the rules."
Salmond has now written again to Heywood demanding an inquiry. He said: "This makes the case for a full inquiry irresistible and … extremely urgent.
There were suggestions this week about the safety of jobs in the financial sector in Scotland.
These turned out to be false, and this was backed up in a statement by RBS chief executive Ross McEwan.
It said: "Any decision to move our registered headquarters should have no impact on everyday banking services used by our customers … This is a technical procedure regarding the location of our registered head office. It is not an intention to move operations or jobs."
Yesterday, it emerged that Edinburgh financier and RBS shareholder Peter de Vink has written to Police Scotland, the City of London Police, the Financial Conduct Authority and the Lord Advocate of Scotland asking for a probe into the release of the information relating to RBS's relocation.
In his complaint he raised concerns of "criminal and inappropriate activities" with impacts on "shareholders, customers and the wider public in Scotland". He told the Sunday Herald: "I feel that the Westminster government has behaved almost like a banana republic dictatorship.
"I am incensed … Scotland could be a great success story as an independent nation."
Last week, Lloyds Banking Group, Clydesdale Bank, Tesco Bank, TSB and Standard Life set out contingency plans post-referendum which included moving aspects of their business - such as headquarters or legal registration - south of the Border. Retailers including Asda, and John Lewis said prices would rise in an independent Scotland.
That was contradicted by others including Tim Martin, the head of Wetherspoon, one of Britain's biggest pub chains, who said Scotland could thrive on its own, and Tesco, which denied claims its prices would rise in an independent Scotland.
Senior banking experts also dismissed claims made yesterday by Deutsche Bank's chief economist David Folkerts-Landau that a Yes vote would cause the kind of instability which triggered the Great Depression of the 1930s.
Ian Blackford, who formerly ran Deutsche Bank's operations in Scotland and the Netherlands, said the argument made about the financial services sector in Scotland benefiting from the strength of the Union failed in light of the fact Deutsche Bank had shut its Edinburgh office in 2005.
HE said: "A business which had been highly successful was trashed and closed in Edinburgh by Deutsche Bank. They are saying there is a risk to the financial industry - yet they did it themselves … under the Union."
Edward McDowell, a former risk manager for Lloyds Banking Group, called the Deutsche Bank warning "totally disingenuous".
He said: "There is no balanced comment around the strong fiscal situation Scotland is in, which is clearly established in situations that are here and will remain here.
"That part of it is not getting across to give people a balanced view and allow them to make a sensible judgment for Thursday."
He decided to speak out after reading reports of risks to jobs from "relocation" of bank head offices. "It is purely a technical issue," he said.
Michelle Thomson, managing director of pro-independence group Business for Scotland, who has held senior roles at Standard Life, said: "Standard Life has managed to still retain a sense of identity and strong Scottish brand - it is headquartered in Edinburgh and has literally thousands of staff. The idea that they would move lock, stock and barrel is ridiculous."