The Justice Department has withheld thousands of documents from the Epstein files, including FBI documents that detailed a woman’s unverified allegations of sexual misconduct against President Trump , according to a review by The Wall Street Journal.

After a Journal analysis identified more than 40,000 files that appeared to be missing from documents posted to the DOJ’s website, a Justice Department spokeswoman said that “47,635 files were offline for further review and should be ready for re-production by the end of the week.”

The withheld files included Federal Bureau of Investigation notes documenting a series of interviews the woman gave to agents in 2019 in which she alleged sexual misconduct by Trump and Jeffrey Epstein when she was a minor in the 1980s, according to copies of the documents reviewed by the Journal. Trump has denied wrongdoing and said the Epstein files “totally exonerated” him.

Those documents are similar to many witness statements with unverified claims that were released by the government in January, raising questions about why they weren’t included with the millions of files made public. The Justice Department was required to release to the public such witness statements, under the Epstein Files Transparency Act.

The woman, who claimed she was abused as a minor by Epstein, was deemed ineligible for the Epstein Victims’ Compensation Program, which paid settlements to more than 130 Epstein victims. Her attorneys at the Bloom Firm declined to comment.

The Justice Department included a summary of the woman’s allegations within the Epstein files in January and a so-called Form 302 from the woman’s first interview in which she alleged that Epstein abused her in South Carolina. It didn’t release three other Form 302s, including the interviews in which she discussed Trump.

The Justice Department hasn’t explained why the Form 302s weren’t released. The department said last week that it was conducting a review to see whether any materials were “improperly tagged in its review process” and, if so, that it would release them. Officials have said that they complied with the law and didn’t withhold documents embarrassing to Trump and that many of the files kept offline contain nudity.

“This is the most transparent Department of Justice in history,” the DOJ spokeswoman said. She said the department was working to address victim concerns and redact personally identifiable information and any images of a sexual nature. She said all responsive documents would be published online once proper redactions are made.

Under the law, the department was required to release most government files, including Form 302s. It could withhold files if they are duplicates; fall under attorney-client privilege; could hurt a continuing investigation; or are completely unrelated to the Epstein and Ghislaine Maxwell cases. The law prohibits the department from withholding or redacting files because they could be embarrassing to public figures.

Democrats in Congress have said they would investigate.

White House spokeswoman Abigail Jackson said: “By releasing thousands of pages of documents, cooperating with the House Oversight Committee’s subpoena request, signing the Epstein Files Transparency Act, and calling for more investigations into Epstein’s Democrat friends, President Trump has done more for Epstein’s victims than anyone before him.”

The documents show the woman, whose name is redacted, had four meetings with Federal Bureau of Investigation agents in 2019, after Epstein was arrested and during Trump’s first term in the White House. She initially made allegations that Epstein sexually abused her and told agents she was reluctant to discuss Trump, the FBI’s notes from the interviews show.

In the interviews, the woman told agents that she was aware that because she was claiming abuse from years earlier, “the statutes of limitation of any viable federal violation may have run. She asked agents, ‘what’s the point?’” according to the documents. Agents reassured her that all victims of crime should have an opportunity to tell their stories.

In her meetings with the FBI, the documents show that the woman detailed her allegations from an encounter she claimed Epstein arranged with Trump in New York or New Jersey when she was about 13 to 15 years old, which haven’t been verified. She was “introduced to someone with money, money…. It was Donald Trump ,” according to the documents. She also claimed to have had two additional interactions with Trump.

Justice Department officials have cautioned that some files include fake or false materials that were sent to the FBI by the public. “Some of the documents contain untrue and sensationalist claims against President Trump that were submitted to the FBI right before the 2020 election,” the department said in a Jan. 30 press release .

The woman joined a Jane Doe lawsuit in 2019 against the Epstein estate, claiming Epstein sexually abused her around 1984 when she was about 13. The lawsuit said Epstein flew her to New York and trafficked her to “prominent wealthy men.” The lawsuit didn’t name the men. Her suit was voluntarily dismissed in 2021.

Write to Sadie Gurman at sadie.gurman@wsj.com and Caitlin Ostroff at caitlin.ostroff@wsj.com