Speaking at a news conference outside Epstein's New York mansion, US Attorney Geoffrey Berman was asked by reporters if the FBI had "reached out" to Prince Andrew as part of its wider investigation into Epstein's sex trafficking case.
Mr Berman said Andrew had been contacted but added: "To date, Prince Andrew has provided zero cooperation."
Andrew 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.”
He was accused of lacking empathy for Epstein's victims and of failing to show regret over his friendship with the disgraced financier.
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. He has strenuously denied the allegations.
Giuffre has said she had sex with Andrew three times at Epstein's request, including once in London in 2001 at the home of Epstein's girlfriend, Ghislaine Maxwell.
Andrew and Maxwell have both denied any knowledge that Epstein, who killed himself in his jail cell last summer while he was awaiting trial on sex trafficking charges, was sexually abusing teenage girls.
In the BBC interview, Andrew insisted he was out at Pizza Express in Woking on the night Giuffre says they were together in London.
US Attorney General William Barr has vowed to aggressively investigate and bring charges against anyone who may have helped Epstein and Andrew has said publicly suggested he would willingly cooperate with an investigation.
Mr Berman made his remarks about the case during a joint appearance with members of Safe Horizon, a nonprofit victim services agency, to discuss a new New York law that made it easier for people to sue over childhood sexual abuse.
He would not discuss the Epstein investigation in detail, but reiterated that the case did not end with his death.
He also confirmed the investigation was looking at possible "conspirators" who worked with Epstein.
"Jeffrey Epstein couldn't have done what he did without the assistance of others, and I can assure you that the investigation is moving forward," he said.
Two guards who were supposed to be monitoring Epstein the night he was found dead have been charged with falsifying the jail's log books to indicate they were performing checks on prisoners, when they were actually sleeping or browsing the internet.