Manhattan federal prosecutors are conducting an “ongoing investigation of uncharged individuals” connected to Jeffrey Epstein, according to court papers filed Thursday.

The probe was revealed in a court filing that seeks to ensure that evidence in the case against Epstein remains secret.

Prosecutors said they planned to give lawyers for the convicted pedophile “certain documents and materials” containing both “confidential” and “highly confidential” information that shouldn’t be made public.

But they asked Manhattan federal Judge Richard Berman to first endorse a nine-page order prohibiting the lawyers from sharing the information with anyone not directly involved in Epstein’s case.

The reasons include the possibility that releasing it “would impede, if prematurely disclosed, the Government’s ongoing investigation of uncharged individuals,” according to the Manhattan federal court filing.

None of those people were identified.

The “highly confidential” information “contains images of nude or partially-nude individuals” that will only be made available to the defense “under the protection of law enforcement officers or employees,” according to court papers.

Prosecutors have said that investigators seized a massive trove of photos of nude photos – including of at least one girl who was underage at the time – during a raid on Epstein’s $77 million Upper East Side townhouse.

Some of the porn was found stashed in a locked safe, along with diamonds, cash and an Austrian passport that Epstein allegedly used to travel during the 1980s to the United Kingdom, France, Spain and Saudi Arabia.

The order filed on Thursday has already been signed by Epstein lawyer Martin Weinberg, who agreed to the prosecution’s terms.

Epstein — who suffered injuries to his neck in a jailhouse incident that remains under investigation — is charged with conspiracy and child sex-trafficking in the alleged sex abuse of dozens of underage girls at his Upper East Side townhouse and waterfront mansion in Palm Beach, Florida, between 2002 and 2005.

His indictment alleges that the multimillionaire financier was assisted by at least three unidentified employees who scheduled his “sexual encounters with minor victims” under the guise of massages for which he paid the girls several hundred dollars each.