The Prince's Trust, founded by Charles in 1976, has a number of celebrity ambassadors who support the charity, which helps disadvantaged young people find employment.
A spokesperson for the Prince's Trust said: "In light of Phillip's recent admissions, we have agreed with him that it is no longer appropriate to work together."
Phillip, 61, confessed to the affair in a statement to the Daily Mail last Friday after announcing his departure from the breakfast show after more than 20 years, writing: "I am making this statement via the Daily Mail to whom I have already apologised personally for misleading, through my lawyer who I also misled, about a story which they wanted to write about me a few days ago. The first thing I want to say is: I am deeply sorry for having lied to them, and to many others about a relationship that I had with someone working on This Morning."
He continued: "I did have a consensual on-off relationship with a younger male colleague at This Morning. Contrary to speculation, whilst I met the man when he was a teenager and was asked to help him to get into television, it was only after he started to work on the show that it became more than just a friendship. That relationship was unwise, but not illegal. It is now over.
"When I chose to come out I did so entirely for my own wellbeing. Nobody 'forced' me out. Neither I nor anyone else, to my knowledge, has ever issued an injunction, super or otherwise, about my relationship with this colleague, he was never moved on or sacked by or because of me."
ITV said it was "deeply disappointed by the admissions of deceit" made by Phillip and confirmed it had cut all ties with the host.
The network said it had investigated rumours of a relationship between the presented and a younger employee in 2020 - but both "repeatedly denied" it.
Phillip, who rose to prominence as a children's BBC presenter in the 1980s, was also dropped by his talent agency YMU.
Meanwhile, Phillip's co-host, Holly Willoughby, 42, responded to Phillip's statement on social media, writing: "It's taken time to process yesterday's news. When reports of this relationship first surfaced, I asked Phil directly if this was true and was told it was not. It's been very hurtful to find out that was a lie. Holly.”
Holly, who usually temporarily departs the show during school holidays, is expected to return to This Morning sofa after the half-term break on Monday 5 June.
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