A move to only fly the Union flag once a year on Scottish government buildings has been criticised by some Tory MPs as "insulting" and an example of "small mindedness".
The decision was taken by the Scottish National Party's administration to reduce the number of days the flag will be flown down from 15.
The British flag will no longer fly on royal birthdays and anniversaries and instead will be unfurled from dozens of government buildings only on Remembrance Sunday.
On other occasions, including the Queen's birthday, it will be replaced by the Scottish Saltire.
"Refusing to fly the Union flag on the Queen's birthday is something that may well appeal to the extreme elements of the nationalist movement," Scottish Tory MSP Murder Fraser said. "But ordinary members of the public will be altogether less convinced."
Fraser added that the decision was "just another example of the SNP government pushing its separatist agenda by stealth".
Meanwhile the new guidance issued by the First Minister's civil servants was described by MPs in Westminster as "outrageous".
"The SNP lost the referendum and they seem to be forgetting this crucial point," said Tory MP Jacob Rees-Mogg.
"This decision smacks of small mindedness and is an affront to the majority of Scots who voted to remain within the UK."
Former Tory leader Iain Duncan Smith slammed the SNP's decision.
"It is insulting to Scottish people to pretend that somehow Scotland is not within the UK. It is a tawdry attempt to sow more division —when will the SNP learn that this is not what the vast majority of the Scottish people want?
"I am sure the vast majority of Scottish people who do want to leave the UK will recognise what a risk the SNP poses to the UK."
The updated guidance applies to buildings operated by Scottish Government and its executive agencies. It will follow the practice kept at the government's St Andrew's House headquarters in Edinburgh, where the British flag is only flown on Remembrance Sunday.
Instead of using the Union flag, the Scottish Government uses the Royal Banner of Scotland, also known as the Lion Rampant, to celebrate royal birthdays and events.
The new rules will not apply to the Holyrood parliament, but must be followed by the government's executive agencies, the Telegraph noted. Only Edinburgh Castle, Stirling Castle and Fort George near Inverness will be allowed to fly the Union flag "on an ongoing basis" due to their British Army presence, a spokesman said.