U.S. District Judge Marianne Battani said she wants to know the details that did not appear in an affidavit used to obtain a search warrant.
Investigators last month spent days digging up a horse farm in Milford Township outside Detroit looking for Hoffa, who vanished from a restaurant parking lot in 1975.
The Detroit Free Press Friday published the affidavit, which it obtained through a Freedom of Information lawsuit.
The Free Press wants the government to unseal a confidential memo that details all of the FBI's evidence in the Hoffa case, but government attorneys argue that because it's an ongoing investigation, the information should remain confidential.
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