KPMG did not renew sponsorship of the Duke of York Entrepreneurship Initiative, Pete Palace.
It is believed that the accounting firm made the decision at the end of October.
The controversy over Prince's ties to convicted sex offender Jeffrey Epstein is understood to be one of the reasons for this decision.
The revelation comes after the BBC's Prince Andrew appeared on Newsnight in what critics called a "car accident" interview.
In the interview, the queen's third child said he still does not regret the friendship with US financier Epstein – who lost his life in August while awaiting trial on US sex trafficking charges.
The BBC contacted Buckingham Palace for comment on KPMG's decision.
The accounting and auditing firm – which is not the only company affiliated with Pitch @ Palace – declined to comment.
The scheme was founded by Prince in 2014 and includes entrepreneurs competing for the chance to direct their business ideas to influential business figures.
The project works in 64 countries and claims to create more than 6,300 jobs.
Meanwhile, Huddersfield University students put forward a proposal to lobby the prince to resign as chancellor on Monday night.
The university itself said that Prince Andrew's "enthusiasm for innovation and entrepreneurship" was "a natural fit" with his work.
The external trust obligation, of which the prince is the patron, said he would hold a special board meeting over the next few days for members to discuss "questions raised" by the interview.
Amid the backlash from a BBC interview on Saturday, Prince Andrew faces renewed calls to tell US authorities about his friendship with Epstein.
The prince said he would testify under oath "if there is pressure to push" and his lawyers advised that.
In an interview with the BBC, Prince Andrew also "categorically" denied having had sex with an American woman who says he was forced to have sex with her at the age of 17.
Virginia Uffufre – one of Epstein's accusers, formerly known as Virginia Roberts – claims she was forced to have sex with the prince three times.
Responding to the claim, the prince said: "I have no memory of ever meeting this lady, not one."
He added that Ms Uffufre's report of him "sweating profusely" and "sweating" when they danced at the club on the night of 2001, when she said having sex for the first time was impossible because he had a medical condition preventing sweat it out.
People close to Prince Andrew said he wanted to address the issues mainly, and he did so with "honesty and humility" in a conversation with the nightlife.
Athonathan Tourley, a law professor at George Washington University, said it was "unlikely" the prince would get an invitation if he went to the United States and the lawyers representing the alleged victims could reach him.
"There are many of these lawyers who would like to invite Prince Andrew [an order to give evidence]"He told the BBC.
But Professor Tourley added that the duke would have had diplomatic immunity if he had been in the United States as part of the royal engagement – rather than personal.
"This interview [has] put him in a rather precarious position if he plans to visit the United States any time soon, "he added.
The prince was reluctant to speak, but former Buckingham Palace Press Officer Dickie Arbiter described the interview as "excruciating".
And the BBC's Royal BBC correspondent Nyoney Dimond said the prince was "very damaged" by the interview, adding that the attempt to clear his name "failed, badly".
A lawyer for several Epstein defendants described the interview as "sad" and "depressing".
Spencer Quinn, who represents several unnamed alleged victims, said "the royal family has failed."
"The very fact that he was a friend of a convicted sex offender and chose to continue his relationship with her – it just shows a lack of recognition of the breadth of what this man [Epstein] he did these girls, "said Mr. Kuvin.
The prince said he visited Epstein in 2010 after being released from prison to tell him that their friendship had ended. He said it was the last contact he ever had with him.