The Duke of York said in a statement that there had been immense speculation about Epstein who apparently killed himself in a New York jail earlier in August while awaiting trial on sex trafficking charges.
"This is particularly the case in relation to my former association or friendship with Epstein. Therefore I am eager to clarify the facts to avoid further speculation."
Andrew said he met Epstein in 1999 and saw him once or twice a year during the time he knew him, and also stayed in several of his residences, the BBC reported.
"At no stage during the limited time I spent with him did I see, witness or suspect any behaviour of the sort that subsequently led to his arrest and conviction.
Video footage emerged this week showing the prince inside Epstein's Manhattan mansion in 2010.
"I have said previously that it was a mistake and an error to see him after his release (from prison) 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," said Andrew.
The duke added that he had "tremendous sympathy" for all those affected by Epstein's behaviour.
"This is a difficult time for everyone involved and I am at a loss to be able to understand or explain Epstein's lifestyle. I deplore the exploitation of any human being and would not condone, participate in, or encourage any such behaviour," said Andrew.
Allegations against Epstein surfaced in 2005 when the parents of a 14-year-old girl told the 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.
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.
( With inputs from IANS )