Boris Johnson reportedly "squared up" to the then-Prince of Wales when the two fell out over Charles' desire to make a speech about slavery.
The explosive confrontation was said to have caused a major rift between the two.
The supposed events were revealed by Guto Harri, Boris Johnson's media chief who served from February to September 2022.
He recalled how the heads of government 'went quite hard', leading to a falling out between the country's future King and the then Prime Minister who was later succeeded by Liz Truss.
'Relations never fully recovered' between Boris Johnson and King Charles, says ex-media chief
Mr Harri said in his newly launched podcast, Uprecedeneted: Inside Downing Street: "Signs of Coronation celebrations are still visible all over central London – the bunting is still up and the Union Jack still hoisted on every flag pole.
"Things were not so celebratory when Boris and the soon-to-be King went to Kigali, Rwanda. Prince Charles, as he was then, had criticised the government's approach to small boats.
"He was also planning a speech on slavery. Boris squared up, confronted him and warned him 'I'd be careful' he said, 'or you'll end up having to sell the Duchy of Cornwall to pay reparations for those who built it.' Relations never fully recovered."
The new podcast is a six-part series that reveals the inner working of the Government from the point of view of the PM's then-media chief.
Mr Harri said: "It's hard to think of a more turbulent period in British politics, with such a fascinating character at the helm. We all saw the scandals but there's so much more to report and we owe it to history to provide the insight and perspective that comes from having a ringside seat on the inside."
"In this gripping political memoir podcast series Guto will take listeners into the rooms where decisions that affected us all are made and shine a light on the inner workings of one of the most turbulent governments we have witnessed in modern history."
The alleged incident was said to have happened when Boris Johnson and (now) King Charles were in Kigali for the Commonwealth Heads of Government Meeting in June of last year.
This came as the UK Government launched its bid to send asylum seekers to Rwanda, prompting criticism.
It was reported that Charles found the plans "appalling".
Clarence House said at the time that Charles is politically neutral.
During a speech to leaders at the summit, the king said: "I cannot describe the depths of my personal sorrow at the suffering of so many, as I continue to deepen my own understanding of slavery's enduring impact."
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