In his letter to Sir Nicholas MacPherson, John Swinney wrote:
It is essential that the public can make a balanced judgement on the referendum debate.
The misinformation presented in this publication places serious doubts over the accuracy of the full Treasury analysis expected later this week and previous Treasury works on Scotland becoming independent.
Mr Swinney continued:
A simple comparison with the 24 departments of the UK Government shows how ludicrous the claim was.
The Scottish Government has no intention of creating 180 government departments or even 180 public bodies as was later claimed by UK Government press officers and special advisers.
There is no mention of this in the Scottish Government's white paper Scotland's Future.
I would appreciate urgent clarity from yourself as to whether this material was approved by you and on what basis and an explanation of how such blatantly false figures came to be presented to the media on behalf of the Treasury.
More top news
The Foreign Secretary described Jeremy Corbyn as a "mugwump" - but what does that obscure word mean?
Readers are shunning e-books in favour of their traditional counterparts, which sold last year at their highest level since 2012.
Glaucoma is the biggest cause of permanent blindness and affects 60 million people around the world - a tenth of whom are completely blind.