Prosecutors say its release would compromise the investigation into Donald J. Trump’s handling of secret documents after he left office. Now a judge must decide.

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By Glenn Thrush, Maggie Haberman, Alan Feuer and Katie Benner

WASHINGTON — The Justice Department objected on Monday to making public the affidavit used to justify the search of former President Donald J. Trump’s home in Florida, saying its release would “compromise future investigative steps” and “likely chill” cooperation with witnesses.

In a 13-page pleading, filed in a federal court in southern Florida in response to requests by The New York Times and other news organizations to make public the evidence included in the document, prosecutors suggested that the department has undertaken a broad, intensive inquiry into Mr. Trump’s handling of some of the most secret documents of the government after he left office.

The prosecutors acknowledged interviewing witnesses in connection with the investigation of Mr. Trump’s retention of the material. They also wrote that releasing the document could compromise the continuing investigation.

“Disclosure of the government’s affidavit at this stage would also likely chill future cooperation by witnesses whose assistance may be sought as this investigation progresses,” prosecutors wrote. They added that releasing the affidavit could harm “other high-profile investigations” as well.

One of the reasons proposed by the government for not releasing the affidavit was to protect the identities of witnesses against death threats. On Monday, prosecutors in Pennsylvania unsealed charges against a man accused of repeatedly threatening to kill F.B.I. agents in the days after Mr. Trump’s property was searched.

The magistrate judge who signed the search warrant, Bruce E. Reinhart, will ultimately decide whether the affidavit should be released. It is unclear when he will rule on the news media’s request.

The legal — and political — aftershocks from the search were still reverberating a week after F.B.I. agents appeared at the resort while the president was at his club in Bedminster, N.J.

Mr. Trump, who has accused Attorney General Merrick B. Garland of conducting a politically motivated “witch hunt” and roughly rifling through his family’s possessions, claimed on Monday that the government “stole my three Passports,” in a post on Truth Social, the online platform he founded.

By late Monday, the Justice Department admitted the error and contacted Mr. Trump’s legal team to retrieve the three passports — two of them expired and the third an active diplomatic passport, according to one of the former president’s lawyers, Evan Corcoran, and a spokesman for the department.

Mr. Garland agreed last week to release the warrant used to search Mr. Trump’s private club, but has resisted attempts to make public the underlying affidavit, a far more sensitive document that should contain, among other things, the reasons prosecutors believe there was probable cause that evidence of a crime could be found at Mar-a-Lago, Mr. Trump’s estate in Palm Beach, Fla.

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