Judge Timothy Kelly signalled scepticism about the administration's arguments for allowing the ban.
Kelly questioned whether criticising the government constitutes a violation of newsroom standards, noting that "a lot of different concepts that have been admitted in the air" to justify the ban.
The US Department of Justice argued that Trump previously put "CNN on notice" with his complaints about "fake news," adding: "Trump doesn't mind negative press stories if he deserves them."
Lawyers for the news organisations said this week that the White House had offered no new evidence to support its repeated claims that the news outlets' reporting has endangered national security.
On Thursday, lawyer Ted Boutros Jr told the judge that national security reporting is important to "hold the government accountable."
Boutrous Jr argued that Trump simply "got up on the wrong side of the bed and declared a ban on" their work because he "does not like the scrutiny" of his administration.
The US president announced a ban against CNN, MS NOW, and Politico on September 18, accusing them of spreading "fake news."
The three organisations sued the US government alleging First Amendment violations, prompting the judge to issue a temporary stay on the ban until deciding on the merits of the lawsuit.
Kelly is scheduled to rule on the legality of the ban on October 13.
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