Epstein was being held at the Manhattan Correctional Center.
At 7.30am a gurney carrying a man who looked like Epstein was wheeled out of the jail, the New York Post reported.
Epstein had faced a trial on the sex trafficking charges next year, with a possible 45-year prison sentence if convicted.
Yesterday, after months of legal wrangling, a Manhattan court had released 1,200 pages of documents detailing lurid claims of the alleged abuse carried out by Jeffrey Epstein on teenage girls.
The files related to the separate civil case of Giuffre v Maxwell, in which Virginia Giuffre, claimed to have been the US businessman’s teenage “sex slave”.
Last month Epstein had been found unconscious in his cell in what appeared to have been a suicide attempt.
Epstein, who was arrested on July 6, had pleaded not guilty to charges of sex trafficking involving dozens of underage girls as young as 14, from at least 2002 to 2005.
The charges were announced more than a decade after Epstein pleaded guilty to state prostitution charges in Florida.