A source close to Andrew told the Daily Telegraph the royal is "happy to talk" to the FBI but has not been approached by them.
It comes after US lawyer Geoffrey Berman said at a news conference in New York on Monday that the duke had not cooperated, claiming his lawyers had been contacted by prosecutors and the FBI as part of the probe.
Buckingham Palace did not comment following the press conference, but it was understood the matter was being dealt with by Andrew's legal team.
But a source told the Telegraph: "The duke is more than happy to talk to the FBI but he hasn't been approached by them yet.
"He is angry about the way this is being portrayed and bewildered as to why this was said in New York."
Virginia Giuffre, who claims she was trafficked by Epstein, said in an interview with BBC Panorama that she was left "horrified and ashamed" after an alleged sexual encounter with Andrew in London in 2001.
Andrew categorically denies he had any form of sexual contact or relationship with Ms Giuffre.
He stepped down from royal duties in November following a disastrous Newsnight interview in the wake of the scandal.
At the time, he said: "I am willing to help any appropriate law enforcement agency."
Following the interview, he was accused of failing to show regret over his friendship with the disgraced financier, who took his own life in prison while awaiting trial on sex trafficking and conspiracy charges.
Mr Berman, who is overseeing the investigation, told reporters outside Epstein's New York mansion that "to date, Prince Andrew has provided zero cooperation".
US lawyer Lisa Bloom, who represents five of Epstein's alleged victims, said lawyer Mr Berman had been left with "no choice" but to comment publicly about Andrew's alleged lack of cooperation because he did not have the power to subpoena the royal as part of the criminal investigation.
Speaking to BBC News on Tuesday, she called on Andrew to "stop playing games" and "do the right thing" by speaking to the authorities to assist with their investigation into the inquiry.