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YMU still represents Amanda Holden and her fellow Britain's Got Talent judge Simon Cowell.
Chris Hughes resigned as a director of the holding company of YMU nearly two months ago, on April 18, according to MailOnline.
He is one of ten directors who have quit the company in the last three years, according to the publication.
The business is also said to have called in trusted advisers to explore financial restructuring after the company made a loss of £4.8 million.
Express.co.uk have approached YMU Group for comment.
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The company - whose name stands for You, Me and Us - is one of the most prominent in the British entertainment industry.
Its former clients include Phillip and This Morning co-presenter, Holly Willoughby, while its current roster comprises figures such as the Saturday Night Takeaway and Britain's Got Talent duo Ant & Dec, Davina McCall and Claudia Winkleman.
The agency issued a scathing statement last month in response to Phil’s shock admission after he confirmed he had an affair with a young male colleague at This Morning.
Mary Bekhait, Group CEO of YMU, said: "This week, we have learned important new information about our client Phillip Schofield. These facts contradicted what Phillip had previously told YMU, as well as the external advisors we had brought in to support him.
"As a result, on Thursday we agreed to part company with Phillip, with immediate effect."
In a statement Phil apologised for lying to his agents, lawyers, ITV colleagues and his family.
He said: "I am painfully conscious that I have lied to my employers at ITV, to my colleagues and friends, to my agents, to the media and therefore the public and most importantly of all to my family.
"I am so very, very sorry, as I am for having been unfaithful to my wife."
Phil revealed that he will no longer have any work on any shows with ITV – such as Dancing on Ice and The Cube.