Andrew stepped down from royal public life in November after the fallout from his disastrous Newsnight appearance, and the Queen cancelled her son’s formal birthday celebrations soon after.

The message was sent by civil servant Matt Stevenson – private secretary to Dame Melanie Dawes, the permanent secretary of the Ministry of Housing, Communities and Local Government.

Councils had been sent an email instructing them to mark the Duke of York’s birthday by flying the union flag on February 19.

Downing Street has been forced into a hasty rethink after complaints about a diktat that town halls should fly a flag for Prince Andrew’s 60th birthday.

Just seen this being debated on @GMB Whilst I’m very supportive of the Royal Family I personally believe it is wholly inappropriate in the prevailing circumstances for Council’s to fly the Union Jack for Prince Andrew’s birthday! @theresa_may @RBWM https://t.co/NAsnJmGyAZ

The prince was accused of showing a lack of empathy for sex trafficker Jeffery Epstein’s victims and of failing to show regret over his friendship with the disgraced financier.

Virginia Giuffre, previously known as Virginia Roberts, claims she was trafficked by convicted sex offender Epstein and alleges the duke slept with her 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.

Perhaps unsurprisingly, the instruction to formally mark his birthday did not prove universally popular.

Tory councillor Phil Haseler, of Windsor and Maidenhead Council, tweeted: “Whilst I’m very supportive of the Royal Family I personally believe it is wholly inappropriate in the prevailing circumstances for councils to fly the Union Jack for Prince Andrew’s birthday!”

Speaking to HuffPost UK, he added: “Allegations of a serious nature have been made against Prince Andrew, as a result of which he has stepped back from public duties.

“He has so far failed to stand up to his responsibilities and make himself available to be interviewed by law enforcement officers.

“As a member of the royal family he should be setting an example not only to the citizens of the UK but to the world, he has so far failed to do so.

“To fly the flag for his birthday would be a sign of respect, Prince Andrew does not command that respect with the behaviour displayed to date.

“It would be highly disrespectful to the complainants and plainly inappropriate to fly the flag for his birthday.”

Meanwhile Liverpool Mayor Joe Anderson told the Liverpool Echo the council would not be flying the flag. He said: “No, we won’t be doing that. I don’t think that would be appropriate.

“This isn’t to do with being anti-royal, we have flown the flag for the Queen before.”

An unnamed council source told The Sun: “Making this gesture while there is a cloud hanging over the duke is hugely insulting to Epstein’s victims and those wanting answers.”

The prime minister’s official spokesperson played down the instruction, saying: “This was an administrative email about long-standing policy.

“I understand DCMS and the royal household are considering how the policy applies in changing circumstances such as when members of the royal family step back from their duties.”