The Queen is facing a million-pound black hole in her estates’ finances after Brexit which has caused consternation among royal aides, The Sunday Telegraph has learned.

Sandringham Estate, the Queen’s country retreat in Norfolk, will lose close to £700,000 a year when EU farming subsidies end while the farms near Windsor Castle will be around £300,000 down.

Prince Charles’s estates are also facing a funding cut from Brexit of £100,000 a year while the Crown Estate – which manages Royal land – will also be hit.

A source familiar with Buckingham Palace’s finances said there had been concerns since before the EU referendum about the impact of losing the grants.

While people were not “throwing their hands in the air in despair” there was anxiety about how the current level of EU farming grants will be sustained, the source said.

They added that the Keeper of the Privy Purse, who looks after the Queen’s finances, would likely be sounding out Government figures – though no meetings are known to have taken place.

Ministers are now under pressure to break their refusal to provide commitments for post-Brexit Britain and publicly say the payments will be continued.

Estates and country houses across Britain as well as farmers benefit from Common Agricultural Policy [CAP] payments – the EU’s system of rural support.