Downing Street's decree that every Government department should fly the Israeli flag in solidarity with the victims of last weekend's terrorist attacks led to an astonishing revolt by civil servants, The Mail on Sunday has learned.

After Ministers gave the order for the flags to be raised last week, permanent secretaries – the most senior officials in Whitehall – were bombarded with complaints by colleagues on the grounds that the Government was 'taking sides'.

While some departments, such as Suella Braverman's Home Office, had an Israeli flag flying by Monday, it took Health Secretary Steve Barclay until Wednesday to persuade civil servants – often nicknamed 'the Blob' – to obey his order.

Whitehall sources say that the flag was then taken down again against Mr Barclay's wishes.

'It was removed by officials,' said a source yesterday. 'We are trying to get it back up again.'

It is also understood that when Mr Barclay said he wanted to bathe the entrance of his department in blue and white – the colours of the Israeli flag – he was told it was not technically possible, despite the rainbow colours of the Pride flag having previously been projected on to the Health Department in solidarity with LGBT rights.

In the end, a compromise was found by illuminating the entrance just in blue.

No 10 led the way in the aftermath of the Hamas attacks by projecting the Israeli flag on to Downing Street and ordering all Government buildings to follow suit.

The flag was also projected on to the Houses of Parliament and London's City Hall, but the Welsh Assembly joined the Scottish Parliament in declining to do so.

A Whitehall source said: 'Despite the horrific nature of the Hamas attacks, there was still a lot of resistance to the idea of flying the flag.

'It was intended as a mark of solidarity with the victims, but civil servants are disproportionately Left-leaning and instinctively sympathetic to the Palestinian cause.

'The perm secs [permanent secretaries] were lobbied hard to block the move on the grounds that it was taking a political side.'

Government departments also flew the Ukrainian flag, or projected its colours – yellow and blue – on to its buildings in the wake of Russia's invasion last year.

The row comes after the Football Association was criticised for refusing to light up Wembley in the Israeli colours for England's friendly with Australia on Friday.

A minute's silence was observed to remember the innocent victims on both sides of the conflict, and players wore black armbands.

Both Israeli and Palestinian flags were banned from the match.

Israel Football Association chief Moshe Zuares has accused the English FA of being 'afraid' to make the tribute, saying: 'There are moments in history when truth is one, sharp and clear. Such is the present time.

'More than 1,200 children, babies, women, men and old people were slaughtered by a barbaric enemy, who committed crimes against humanity. The only sin of the victims was that they were Israelis.

'Those who are afraid to light up a stadium in memory of the murdered and for the sake of historical truth, for reasons that cannot be understood at all and perhaps it is better not to even try, are in an even darker time than the one in my country is currently in.'

Ms Braverman has warned that waving a Palestinian flag on British streets 'may not be legitimate' if it is deemed to support terrorism.