Prince Andrew was reportedly appalled at the allegations of sexual abuse surrounding Epstein after a video was released of him at the home of the convicted paedophile in 2010.
"The Duke of York has been appalled by the recent reports of Jeffrey Epstein’s alleged crimes," Buckingham Palace said in a statement on Monday.
"His Royal Highness deplores the exploitation of any human being and the suggestion he would condone, participate in or encourage any such behaviour is abhorrent."
Virginia Giuffre — previously Virginia Roberts — testified that she was forced to have sex with Prince Andrew in London when she was 17.
The woman said she had sex with him again in New York and on Epstein’s private island in the Caribbean, but the allegations were struck from the record by a US judge in 2015, who said the "lurid details" were not needed to decide a civil case concerning Epstein.
Buckingham Palace has repeatedly denied the claims, calling them "false and without foundation."
At the Davos annual meeting in 2015, Prince Andrew referred to the allegations, saying: "I wish to reiterate and reaffirm the statements already made on my behalf by Buckingham Palace. My focus is my work."
The Duke of York was forced to resign as Britain's special representative for international trade and investment in 2011 after scrutiny over his relationship with Epstein.
The Sun reported that Sarah Ferguson took a "panicked" Andrew to Spain for a holiday after he left his break at Balmoral early.
"The Duchess insisted she go on holiday with the Duke to look after him and show the world she stands by him," said a royal insider.
The insider revealed that the 59-year-old is starting to "sh*t himself" over the attention following Epstein’s death in a New York jail while awaiting trial for sex trafficking.
"The Duke has been fairly relaxed up to now, he’s starting to sh*t himself.
"It’s become the biggest story in the world and he’s at the heart of the coverage."
The testimony of a second accuser, Johanna Sjoberg, was also revealed in the court documents.
The woman claimed that Prince Andrew groped her at a party at Epstein’s New York mansion in 2001, and made sexual advances to her and Virginia Giuffre using a "Spitting Images" puppet that looked like him.
Prince Andrew has strenuously denied any wrongdoings.
A Palace spokesman said: "This relates to proceedings in the United States, to which The Duke of York is not a party. Any suggestion of impropriety with underage minors is categorically untrue.
"It is emphatically denied that The Duke of York had any form of sexual contact or relationship with Virginia Roberts. Any claim to the contrary is false and without foundation."