In a statement, the Duke of York said he wanted to "clarify the facts" around his "former association or friendship" with the US financier.
He said it was a "mistake" to meet Epstein after he left prison in 2010.
"During the time I knew him, I saw him infrequently and probably no more than only once or twice a year," the prince said.
"I have stayed in a number of his residences. At no stage during the limited time I spent with him did I see, witness or suspect any behavior of the sort that subsequently led to his arrest and conviction."
The duke - who said he first met Epstein in 1999 - added that he had "tremendous sympathy" for all those affected by Epstein's behavior.
"His suicide has left many unanswered questions and I acknowledge and sympathize with everyone who has been affected and wants some form of closure." Allegations against Epstein surfaced in 2005 when the parents of a 14-year-old girl told police in Florida he had molested their daughter at his Palm Beach home.
The financier was accused of paying underage girls to perform sex acts at his Manhattan and Florida mansions between 2002 and 2005.
A controversial secret plea deal saw him plead guilty to a lesser charge of soliciting a minor for prostitution. He received an 18-month prison sentence and was released on probation in 2010.
Prince Andrew was photographed with Epstein in New York's Central Park in late 2010 - after the tycoon was released from jail.
Footage has also emerged reportedly showing the prince at Epstein's mansion in Manhattan in 2010.
In the statement, released on Saturday, the duke added: "I have said previously that it was a mistake and an error to see him after his release in 2010 and I can only reiterate my regret that I was mistaken to think that what I thought I knew of him was evidently not the real person, given what we now know.
"This is a difficult time for everyone involved and I am at a loss to be able to understand or explain Mr. Epstein's lifestyle.
"I deplore the exploitation of any human being and would not condone, participate in, or encourage any such behavior."
In July 2019 Epstein was charged in New York with further allegations of sex trafficking and conspiracy and was due to face trial next year. He pleaded not guilty to all the charges but if convicted, was facing up to 45 years in prison.
Prince Andrew and Jeffrey Epstein: Key dates
Feb 1999 - The Duke of York said he first met Epstein, a wealthy hedge fund manager, in 1999. Prince Andrew reportedly flew with Epstein on his private Gulfstream jet in February that year, according to the Daily Mirror.The Daily Mail also reported that 10 months earlier Epstein's logbook showed he had flown to the same location to meet the duke's ex-wife, Sarah Ferguson.
June 2000 - Epstein and his British ex-girlfriend Ghislaine Maxwell were among a star-studded guest list at a party hosted by the Queen in June 2000. The duke became part of the social circle of Ms. Maxwell - someone who Epstein later described as his best friend. The duke accompanied Ms. Maxwell - daughter of the late newspaper tycoon, Robert Maxwell - at private parties and celebrity functions both in the UK and in the US that year.
December 2000 - The then 40-year-old prince, threw Ms. Maxwell a surprise birthday party at Sandringham, with Epstein among the guests.
December 2010 - The duke met Epstein in New York's Central Park after the tycoon was released from prison. Prince Andrew later said the meeting was a mistake and an error of judgment. Buckingham Palace said he had no contact with Epstein after that.
July 2011 - The palace confirmed the duke would stand down as the UK's trade envoy following criticism of his friendship with Epstein.
2 Jan 2015 - In response to the duke being named in court papers as part of a US civil case against Epstein, the palace said: "Any suggestion of impropriety with underage minors is categorically untrue." According to the Guardian, one of Epstein's accusers, Virginia Roberts - now Virginia Giuffre - said she was ordered to give the prince "whatever he required". Buckingham Palace said: "This relates to proceedings in the United States to which the Duke of York is not a party."
3 Jan 2015 - A second statement issued two days later, after further details about allegations were published in Sunday newspapers, stressed claims made about the duke were "without any foundation". "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."
22 Jan 2015 - Prince Andrew spoke about the claims at a World Economic Forum reception in Davos, Switzerland. He said: "I just wish to reiterate and to reaffirm the statements that have already been made on my behalf by Buckingham Palace. My focus is on my work."
August 2019 - In response to questions following Mr. Epstein's subsequent arrest in 2019, a spokesperson for Buckingham Palace said: "The Duke of York has been appalled by the recent reports of Jeffrey Epstein's alleged crimes. His Royal Highness deplores the exploitation of any human being and the suggestion he would condone, participate in or encourage any such behavior is abhorrent."
The duke had been appointed the UK's special representative for international trade and investment in 2001 after retiring from the Royal Navy.
He worked for - but did not receive a salary from - the government body UK Trade & Investment (UKTI), which reports jointly to the Foreign Office and the Department for Business, Innovation, and Skills.
BBC
PRINCE Andrew is “frustrated” because he fears he will not be able to return to the US due to the Jeffrey Epstein scandal, reports claim.
The Duke of York is reportedly worried he may be drawn into the multi-million dollar lawsuits brought by some of his paedo pal’s alleged victims.
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Andrew and Virginia Giuffre - then Roberts - who in 2015 claimed Andrew slept with her three times credit: Rex Features
Andrew has not visited the US since early 2017 – despite the country being one of his “favorite” places in the world to go.
He is said to be “disappointed” that his plans to launch a business scheme for entrepreneurs in the US later this year have been put on hold.
One source told the Daily Mail: “Andrew has openly said he can’t see how he can go back to the US at the moment with everything that is going on.
“I know this is a source of enormous frustration for him as it is one of his favorite places in the world to go.”
Andrew had wanted to get a foothold in the US by taking his Pitch@Palace scheme – a Dragons’ Den-style initiative for entrepreneurs – to the country.
He is understood to have discussed his plans with Donald Trump when the US President came to the UK for his state visit earlier this year.
But the proposal has been “put on ice”, according to reports.
“Andrew is very disappointed as he has long been very keen to get a foothold out there with it,” the source added.
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