"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 statement read.
The Duke of York broke his silence about his relationship with Epstein after a video was published by Britain's Mail on Sunday appearing to show him inside Epstein's Manhattan mansion around the same time the pair were photographed together in 2010 in New York City's Central Park.
NBC News has not authenticated the video and Buckingham Palace did not specifically comment on it.
Epstein died by suicide at age 66 in his Manhattan jail cell on Aug. 10 after being held on federal child sex-trafficking charges. Prosecutors claimed he sexually abused dozens of underage girls in New York and Florida.
Prince Andrew, who is the third child of Queen Elizabeth II, has previously faced accusations related to Epstein's alleged sex trafficking ring, including in a 2015 defamation lawsuit filed by Virginia Giuffre.
In the suit, Giuffre alleged that Epstein forced her to have sex with Andrew on three separate occasions when she was 17 years old. Andrew has denied the allegations and the lawsuit was settled out of court.
Epstein's attorneys announced over the weekend that they're "not satisfied" with the medical examiner's report that ruled Epstein's death a suicide by hanging at the Metropolitan Correctional Center.
"It is indisputable that the authorities violated their own protocols,'' his defense team told NBC News. "The defense team fully intends to conduct its own independent and complete investigation."
His lawyers also said they are prepared to take legal action to obtain videos possibly showing the moments before Epstein's death inside his cell.
Some of the employees at the correctional facility where he died have not submitted to interviews by the FBI and the Justice Department's inspector general and some have retained lawyers, a Justice Department official told NBC News.