In a strongly worded statement the Prince said it would be "ludicrous" to believe the "outrageous and hurtful" claims made in the LWT documentary, Charles At 50, to be screened tomorrow evening.
The rare joint statement from Buckingham Palace and St James's Palace said the Prince, who is in Bulgaria, telephoned the Queen in the afternoon to say how distressed he was by the reports.
He moved quickly to dissociate himself from publicity material issued by LWT to flatly deny the suggestion that he would be privately "delighted if the Queen were to abdicate". He said: "I begin to tire of needing to issue denials of false stories about all manner of thoughts which I am alleged to be having.
"Some stories are so preposterous that they barely warrant a denial. However, others are both so outrageous and hurtful to my family, to the monarchy and to me personally, that they demand a response. The claims made in LWT's press notice are not only deeply offensive but completely wrong. They in no way reflect my views."
The strength of the Prince's tone was unprecedented and surprised even his closest aides but is a further sign of an increasingly robust attitude by the Royal Family to rumour and tabloid speculation.
"There is no one with a greater sense of duty and loyalty than The Queen. The Queen will always have my abiding admiration and affection and any suggestion that I wish Her Majesty to abdicate is utterly ludicrous."
The statement comes just two weeks after he released a joint statement with his longtime love, Camilla Parker Bowles, after revelations in a new book by Penny Junor.
The Prince made clear then that the book was not authorised, solicited or approved by the couple. The LWT programme also claims that even if the Prince marries Mrs Parker Bowles, she will never become Queen. Instead, the Princess Royal would become the King's Royal Partner, accompanying him on official engagements and representing the Crown on trips abroad.
A spokeswoman for LWT said it stood by the programme, which was based on a series of briefings with a senior Palace aide. "There were four separate briefings. We specifically asked for information on the Prince of Wales's thinking on the future of the Monarchy.
"These briefings were attended by two senior members of the production team who took detailed notes.
"The key points in the briefing were reiterated at least twice and were checked again as recently as this week."
She added that LWT would not be disclosing the name of the senior Palace aide the programme producers spoke to.
The Prince believes the monarchy needs radical modernising and that he, not the Queen, is the person to do this, the programme says.
He is reported as wanting to streamline the Royal Family, with the Duke of York and Prince Edward becoming "non-working Royals" and no longer receiving public money. The monarchy would become self-financing, with income from the Crown Estate replacing income from the Civil List.
The Crown Estate was surrendered to the government more than 200 years ago, but would be transferred back to the crown. And Windsor would become the official Royal residence, while the new Prince of Wales, Prince William, would move to Highgrove.
But all his plans are on hold until he becomes King, and he wants to be King now, LWT claimed in its press material.