"The current proposed protect order throws an unnecessarily broad cloak of secrecy over document and information to be disclosed in discovery," the document wrote.
The judge explained the protective order is not necessary for circumstances where a conspiracy began and ended several years ago, the document said. Manafort's case involved charges of engaging in conspiracies that began as long ago as 2005 and ended in 2014, the document added.
On Monday, the Special Counsel issued a motion for a protective order on all material provided by the United States in preparation in the Manafort case, according to a separate court document.
Earlier in the day, The New York Times reported that Donald Trump's former lawyer John Dowd discussed the possibility of pardoning ex-Trump advisers Michael Flynn and Paul Manafort.
Three people with knowledge of the discussions told the media that Dowd talked to lawyers for Flynn and Manafort last year about having Trump pardon them.
When asked about the conversations, Dowd denied discussing pardons with the lawyers for Flynn or Manafort.
Trump's current lawyer, Jay Sekulow, told the Times, "Never during the course of my representation of the president have I had any discussions of pardons of any individual involved in this inquiry."
In December, Flynn pleaded guilty for lying to the FBI about his contacts with Russian officials and agreed to cooperate with Special Counsel Robert Mueller's investigation.
Mueller is investigating Russia's alleged meddling in the 2016 US presidential election, as well as accustations of collusion between Moscow and the Trump campaign ahead of the vote.
Russian officials have denied all allegations of interference, calling the accusations "absurd." Trump has also denied any collusion between himself and the Kremlin and has called Mueller's investigation a "witch hunt."