The submission by the Justice Department — which contains proposed redactions and a supporting memo — is a significant legal milepost in an investigation that has swiftly emerged as a major threat to Mr. Trump, whose lawyers have offered a confused and at times stumbling response. But it is also an inflection point for Attorney General Merrick B. Garland, who is trying to balance protecting the prosecutorial process by keeping secret details of the investigation, and providing enough information to defend his decision to request a search unlike any other in history.

“There are clearly opposed poles here,” said Daniel C. Richman, a former federal prosecutor and a law professor at Columbia University, who said it might be difficult, even impossible, for Mr. Garland to strike the right balance.

Last week, Bruce E. Reinhart, a federal magistrate judge in Florida, surprised prosecutors by saying he was inclined to release portions of the affidavit at the request of news organizations, including The New York Times, after the government proposed redactions.

Disclosing even a partial version of the affidavit would be highly unusual: Such documents, which typically include evidence gathered to justify the search, like information provided by witnesses, are almost never unsealed before the government files criminal charges. There is no indication the Justice Department plans to file charges anytime soon.

Judge Reinhart reiterated this week that he might agree to extensive redactions, acknowledging that they could be severe enough to render release of the final document meaningless.

“I cannot say at this point that partial redactions will be so extensive that they will result in a meaningless disclosure, but I may ultimately reach that conclusion after hearing further from the government,” he wrote in an order issued on Monday.