KPMG has not renewed its sponsorship of the Duke of York's entrepreneurship scheme.
The accountancy firm is thought to have made the decision at the end of October, when its sponsorship of [email protected] ended.
The controversy over the duke's ties to the convicted sex offender Jeffrey Epstein is understood to have been one reason behind the move.
It follows what critics called a "car crash" interview with BBC Newsnight.
In the interview, the prince - the Queen's third child - said he still did not regret his friendship with US financier Epstein - who took his own life in August while awaiting trial on sex-trafficking charges in the US.
The BBC has contacted Buckingham Palace for comment regarding KPMG's decision not to renew sponsorship of [email protected]
Accountancy and auditing firm KPMG - which is not the only company associated with the scheme - declined to comment.
[email protected] was founded by the prince in 2014 and involves entrepreneurs competing for the chance to pitch their business ideas to influential business figures at St James's Palace.
The project operates in 64 countries and claims to have created more than 6,300 jobs.
Meanwhile, University of Huddersfield students discussed a motion to put pressure on the prince to resign as chancellor on Monday evening. Their decision will be announced in the coming days.
In response, the university itself said Prince Andrew's "enthusiasm for innovation and entrepreneurship" was a "natural fit" with its work.
Amid the backlash from the BBC's interview on Saturday, Prince Andrew is facing renewed calls to tell US authorities about his friendship with US financier Epstein.
The prince said he would testify under oath "if push came to shove" and his lawyers advised him to.
In his BBC interview, Prince Andrew also "categorically" denied having any sexual contact with an American woman, who says she was forced to have sex with him aged 17.
Virginia Giuffre - one of Epstein's accusers, previously known as Virginia Roberts - claimed she was forced to have sex with the prince three times.
Responding to the allegation, the prince said: "I have no recollection of ever meeting this lady, none whatsoever."
He added Ms Giuffre's account of him "profusely sweating" and "pouring with perspiration" when they danced at the club on the night in 2001 when she says they first had sex was impossible, because he had a medical condition preventing him from perspiring.
People close to Prince Andrew said he wanted to address the issues head-on and did so with "honesty and humility" in speaking to Newsnight.
The prince has stood by his decision to speak out, but former Buckingham Palace press officer Dickie Arbiter described the interview as "excruciating".
And BBC royal correspondent Jonny Dymond said the prince was "very damaged" by the interview, adding the opportunity to clear his name had "failed, badly".
A lawyer for several of Epstein's accusers described the interview as "sad" and "depressing".
Spencer Kuvin, who represents several unnamed alleged victims, said "royalty has failed them".
"The mere fact that he was friends with a convicted sex offender and chose to continue his relationship with him - it just shows a lack of acknowledgement of the breadth of what this man [Epstein] did to these girls," Mr Kuvin.