An order to councils to fly the Union flag on the Duke of York's birthday has been criticised as "crass and offensive".
Local authorities have been told to fly the flag for Andrew's 60th birthday on February 19.
Matt Stevenson, private secretary to Ministry of Housing, Communities and Local Government permanent secretary Dame Melanie Dawes, reminded the councils in an email seen by The Sun.
But critics said that the order should be scrapped because of allegations that Andrew slept with Virginia Giuffre, who claims she was trafficked by convicted sex offender Jeffrey Epstein.
Ms Giuffre, previously known as Virginia Roberts, says she and the Duke slept together on three separate occasions, including when she was 17 - still a minor under US law.
Andrew, who strenuously denies the allegations, is facing calls to talk to the FBI and US prosecutors.
The story prompted a strong reaction from Ms Giuffre.
She wrote on Twitter: "Oh mummy they didn’t even raise the flag on my birthday- if only life was so hard."
She went on to urge the Prince to "get over" himself and to "tell the truth."
Labour MP Ian Murray, who is running to be deputy leader of the party, blasted the proposed flag raising.
“This protocol has to be binned given the allegations against the Prince," he told The Sun.
Republic, a campaign to replace the monarchy with an elected head of state, said councils had better things to worry about than "daft royal protocols".
Republic CEO Graham Smith said: "This is crass and offensive, and that even at the best of times it's nonsense to be flying flags for Andrew's or anyone else's birthday.
"Councils are struggling to provide core services, they have better things to worry about than daft royal protocols.
"And to think we should be celebrating a man who has serious accusations of sexual assault hanging over his head is particularly appalling.
"It's time we ended the whole nonsense of flying flags for royal birthdays.
"It's inappropriate in a democracy and the public aren't interested. I think we'd all rather see councils spend their time and money getting services delivered."
Andrew stepped down from royal public life in November after the fallout from his disastrous Newsnight appearance.
He was accused of showing a lack of empathy for Epstein's victims and of failing to show regret over his friendship with the disgraced financier.
A spokesperson for the prime minister said: "This was an administrative email about a long-standing policy.
"I understand DCMS and the royal household considering how the policy applies to members of the royal family who have stepped back from public duties."
