Deputy Attorney-General Todd Blanche pledged the administration eventually would meet its obligation under a law passed by Congress.
But he stressed the department was obligated to act with caution as it goes about making public thousands of documents that can include sensitive information.
Friday's partial release of the Epstein files has led to a new crush of criticism from Democrats who have accused the Republican administration of trying to hide information.
Blanche called that pushback disingenuous as President Donald Trump's administration continues to struggle with calls for greater transparency, including from members of his political base, about the government's investigations into Epstein, who once counted Trump as well as several political leaders and business titans among his peers.
"The reason why we are still reviewing documents and still continuing our process is simply that to protect victims," Blanche told NBC.
"So the same individuals that are out there complaining about the lack of documents that were produced on Friday are the same individuals who apparently don't want us to protect victims."
Blanche's comments were the most extensive by the administration since the file dump, which included photographs, interview transcripts, call logs, court records and other documents.
But some of the most consequential records expected about Epstein were nowhere to be found, such as FBI interviews with survivors and internal Justice Department memos examining charging decisions.
Those records could help explain how investigators viewed the case and why Epstein was allowed in 2008 to plead guilty to a relatively minor state-level prostitution charge.
Trump, who was friends with Epstein for years before the two had a falling-out, tried for months to keep the records sealed.
Though Trump has not been accused of wrongdoing in connection with Epstein, he has argued there is nothing to see in the files.
Federal prosecutors in New York brought sex trafficking charges against Epstein in 2019, but he killed himself in jail after his arrest.
Democrats see a cover-up, not an effort to protect victims
Representative Jamie Raskin argued the Justice Department is obstructing the implementation of the law mandating the release of the documents.
"It's all about covering up things that, for whatever reason, Donald Trump doesn't want to go public, either about himself, other members of his family, friends, Jeffrey Epstein, or just the social, business, cultural network that he was involved in for at least a decade, if not longer," he told CNN.
Blanche also defended the department's decision to remove several files related to the case from its public webpage, including a photograph showing Trump, less than a day after they were posted.
The missing files, which were available Friday but no longer accessible by Saturday, included images of paintings depicting nude women, and one showed 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.
Blanche said the documents were removed because they also showed victims of Epstein. The Trump photo and the other documents would be reposted once redactions are made to protect survivors.
"It has nothing to do with President Trump," Blanche said.
"There are dozens of photos of President Trump already released to the public seeing him with Mr Epstein."
The thousands of Epstein-related records posted publicly offer the most detailed look yet at nearly two decades worth of government scrutiny of Epstein's sexual abuse of young women and underage girls.
The Justice Department has just learned the names of more potential victims as it continues to review the trove of documents, Blanche said.
