The missing files, which were available on Friday and no longer accessible by Saturday, included images of paintings depicting nude women and one showing a series of photographs along a credenza and in drawers.
In that image, inside a drawer among other photos, was a photograph of Trump, alongside Epstein, Melania Trump and Epstein's longtime associate Ghislaine Maxwell.
The Justice Department did not say why the files were removed or whether their disappearance was intentional.
Online, the unexplained missing files fuelled speculation about what was taken down and why the public was not notified, compounding long-standing intrigue about Epstein and the powerful figures who surrounded him.
Democrats on the House Oversight Committee pointed to the missing image featuring a Trump photo in a post on X, writing: "What else is being covered up? We need transparency for the American public."
The episode deepened concerns that had already emerged from the Justice Department's much-anticipated document release.
The tens of thousands of pages made public offered little new insight into Epstein's crimes or the prosecutorial decisions that allowed him to avoid serious federal charges for years, while omitting some of the most closely watched materials, including FBI interviews with victims and internal Justice Department memos on charging decisions.
Some of the most consequential records expected about Epstein are nowhere to be found in the Justice Department's disclosures, which span tens of thousands of pages.
Missing are FBI interviews with survivors and internal Justice Department memos examining charging decisions - records that could have helped explain how investigators viewed the case and why Epstein was allowed in 2008 to plead guilty to a relatively minor state-level prostitution charge.
The records, required to be released under a law passed by Congress, hardly reference several powerful figures long associated with Epstein, including Britain's former Prince Andrew, renewing questions about who was scrutinised, who was not, and how much the disclosures truly advance public accountability
Among the fresh nuggets: insight into the Justice Department's decision to abandon an investigation into Epstein in the 2000s, which enabled him to plead guilty to that state-level charge, and a previously unseen 1996 complaint accusing Epstein of stealing photographs of children.
The releases so far have been heavy on images of Epstein's homes in New York City and the US Virgin Islands, with some photos of celebrities and politicians.
There was a series of never-before-seen photos of former President Bill Clinton but fleetingly few of Trump.
Both have been associated with Epstein, but both have since disowned those friendships. Neither has been accused of any wrongdoing in connection with Epstein and there was no indication the photos played a role in the criminal cases brought against him.
Despite a Friday deadline set by Congress to make everything public, the Justice Department said it plans to release records on a rolling basis. It blamed the delay on the time-consuming process of obscuring survivors' names and other identifying information. The department has not given any notice when more records might arrive.
That approach angered some Epstein accusers and members of Congress who fought to pass the law forced the department to act.
Instead of marking the end of a years-long battle for transparency, the document release was merely the beginning of an indefinite wait for a complete picture of Epstein's crimes and the steps taken to investigate them.
Many of the long-anticipated records were redacted or lacked context
The documents just made public were a sliver of potentially millions of pages records in the department's possession.
Trump's Republican allies seized on the Clinton images, including photos of the Democrat with singers Michael Jackson and Diana Ross. There were also photos of Epstein with actors Chris Tucker and Kevin Spacey, and even Epstein with TV newscaster Walter Cronkite.
The meatiest records released so far showed that federal prosecutors had what appeared to be a strong case against Epstein in 2007 yet never charged him.
