The grand jury returned a single felony solicitation of prostitution charge, and Epstein pleaded not guilty.
Epstein was arrested on Saturday evening, multiple USA media reported, citing law enforcement sources.
This July 27, 2006 arrest file photo made available by the Palm Beach Sheriff's Office, in Florida, shows Jeffrey Epstein.
Epstein will be held in federal custody in Manhattan until his appearance in court on Monday when the case against him will be unsealed, the person said.
Criminal defense lawyer Gene Rossi told Law&Crime that it was "extremely bad news" for Epstein that the case was being handled by the Southern District of New York's Public Corruption Unit because "they don't play nice".
Epstein's 13-month sentence was one of the most lenient seen in US history for a serial sex offender.
The billionaire is being charged with a single count of sex trafficking minors and an additional count of engaging in the sex trafficking of minors, which could ultimately lead to a jail sentence of up to 45 years.
Epstein, a wealthy financier accused of sexually abusing dozens of teenage girls, struck a controversial plea deal in 2008 under which he served only 13 months in jail, and reached financial settlements with many of his alleged victims. The billionaire sex offender, who served 13 months in an "open-door" prison for abusing scores of underage girls after his lawyers clinched a hush-hush non-prosecution agreement in 2007, might now have to spend the rest of his life in prison.
His obligations to register as a sex offender were also eased because when he pleaded guilty, the only minor he was convicted of soliciting was 16 years old at the time the offenses began.
Some girls were also allegedly brought to Epstein's homes in New York City, New Mexico and a private Caribbean island, according to court documents.
Epstein has said that his encounters with alleged victims were consensual and that he believed they were 18 when they occurred.
The charges, contained in a sealed indictment, involve alleged sex trafficking crimes committed between 2002 and 2005, according to law enforcement sources.
Featuring prominently in the contact details was former US President Bill Clinton and members of his staff, for whom Epstein had a total of 21 numbers.
Democrats in the U.S. House of Representatives confronted Acosta about his role in the Epstein case in April when the labor secretary appeared before the House Appropriations subcommittee on a routine budget matter.
The victims of the "Epstein pedophile ring" were kept in the dark about the deal.
In February, US District Court Judge Kenneth Marra ruled that federal prosecutors broke the law when they signed the plea bargain with Epstein for his 2008 conviction.
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