The newsreader, who broke news of the Queen Mother's death to BBC viewers, said he was leaving the corporation because of "incompatibility" with his colleague Kate Silverton.
Hayton, 57, who was called the "housewives' favourite" while presenting the flagship Nine O'Clock News, has left his role on the News 24 channel after failing to resolve the issue with BBC bosses.
He had been presenting the 9am to 1pm weekday slot with Silverton - who started her working life as a City corporate financier before moving to television - for less than three months. Hayton said: "It boils down to incompatibility. We did four hours of live TV every day and you have to like each other.
"I think incompatibility sums it up and I don't think she would disagree with that. I have been at the BBC for 37 years and it is the first time I have had a problem like this. Maybe it is just the law of averages."
The presenter, who also anchored the 1pm and 6pm bulletins on BBC1 before becoming the latest middle-aged male newsreader to vacate the main channel, said he was leaving the corporation "without bitterness or rancour".
Silverton's agent hit back at Hayton's claims, saying the 35-year-old presenter, a veteran of daytime television, had been unaware of any strains in their professional relationship.
Alex Armitage said: "I think this says more about Philip than it does about Kate. This has come out of the blue. Kate had absolutely no idea about it. She has never had a problem with any other co-presenter."
Silverton, a graduate from Durham University who gained her journalistic grounding in regional television, has also worked for channel Five's The Wright Stuff and co-hosted Weekend with Rod Liddle and Kate Silverton, an ill-fated attempt by the BBC to make politics attractive to a young audience.
The presenter has had to deal with her fair share of critics pigeon-holing her as the latest manifestation on British screens of the American taste for attractive female newsreaders.
One critic said waspishly that she looked "not only as if she had come fresh from a beauty salon but as if she usually worked in one".
But Mr Armitage said Silverton was a proven journalist who had worked for Sky News, BBC Radio 5 Live and had co-hosted BBC1's Breakfast Show. "Anyone who thinks you can't do entertainment as well as news is a dreadful snob."
Hayton, who began his career in pirate radio, covered the Iranian revolution, the overthrow of Idi Amin and the death of General Franco.
The BBC refused to comment on his remarks but pointedly defended Silverton's reputation.
A spokeswoman said: "Philip has chosen to leave the full-time employment of the BBC. He may continue to work for us as a freelancer. Kate is an incredibly professional and popular presenter with the BBC."
Anchors at war
* FRANK PARTRIDGE AND KAY BURLEY
During a row over who would deliver the final words of a bulletin Partridge slapped his co-presenter and former lover. The force sent her head into a door, bruising her jaw. Partridge insisted the blow was accidental but was sacked from his £130,000-a-year job.
* ANTHEA TURNER AND EAMONN HOLMES
The golden pairing of breakfast TV ended after Holmes dubbed Turner "unbearable". Holmes claimed he delivered an ultimatum that either Turner or he leave. Turner left but managers denied they caved in to the ultimatum.
* CHRIS MANN AND SCOTT CHISHOLM
The presenters came to blows off-air after a row, allegedly over which was chief presenter. Chisholm claimed he hit Mann for being rude to his wife, also a presenter. Both men were summarily sacked.
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