The accusation was revealed in a 2016 deposition unsealed on Friday.
The victim, with Virginia Giuffre, said she was also instructed to have sex with former New Mexico Governor Bill Richardson, Prince Andrew of Britain and other prominent men, the VentureBeat reported on Friday.
At the time of the incident, the alleged victim was 17 while Minsky was 73, according to The Verge.
In July, the US Attorney's Office - Southern District of New York indicted Epstein on multiple charges and accused of running a sex trafficking operation of underage girls, the VentureBeat report added.
He was known to be closely associated with prominent politic including incumbent US President Donald Trump and also former President Bill Clinton.
Minsky, who died in 2016, was a noted American cognitive scientist concerned largely with the research of AI, co-founder of the MIT's AI laboratory and author of several texts concerning AI and philosophy.
He was known as a close associate of Epstein, however, this is the first direct accusation implicating him in the Epstein's sex trafficking network.
Epstein is a convicted sex offender and financier who began his career in finance at the investment bank Bear Stearns, before forming his own company named J. Epstein & Co.
( With inputs from IANS )