A federal judge in Hawaii put a temporary nationwide halt to key parts of President Donald Trump's new travel ban Wednesday just hours before it was set to take effect, dealing another significant setback to the administration's highest profile initiative.

U.S. District Judge Derrick Watson blocked provisions of the March 6 executive order that would have frozen the refugee program for 120 days and largely stopped citizens of six majority Muslim nations – Iran, Libya, Somalia, Sudan, Syria and Yemen – from entering the U.S. for 90 days.

On Thursday morning, a district judge in Maryland, ruling on a similar challenge to the travel ban, issued a second temporary restraining order that also stayed the 90-day suspension of entry by citizens of the six designated nations.

Other sections of the executive order, such as a reduction in the number of refugees allowed to resettle in the U.S. from 110,000 to 50,000, were allowed to go forward when the order took effect at 12:01 a.m. Thursday.

Trump excoriated Watson's decision on Wednesday,declaring at a rally that night in Nashville, Tennessee, that the judge's ruling represented "unprecedented judicial overreach."

"The order that he blocked was a watered down version of the first order," Trump said. "We're talking about the safety of our nation, the safety and security of our people."

He added: "This order makes us look weak," and vowed "to fight this terrible ruling."

Watson's ruling was the first to be issued on a whirlwind day that saw four sets of arguments in three federal courthouses across the country.

Minutes after the decision was handed down, U.S. District Judge James Robart, the federal judge in Seattle responsible for freezing Trump's first travel ban Feb. 3, ruled that he would not apply his prior preliminary injunction to the new travel restrictions, finding that the two executive orders were sufficiently different.

However, Robart had not made a decision in a separate challenge to the revised travel ban as of Thursday morning.

Justice Department lawyers had argued that the restrictions amounted to a temporary pause, one that would allow authorities to review immigration and refugee screening procedures and was within the purview of the executive branch. They also rejected arguments that the executive order constituted discrimination against Muslims, emphasizing that the administration had worked to address the concerns raised about the original order.

Drawing on statements by the president, his surrogates and members of his administration, however, Watson rejected contentions that the travel ban was religiously neutral and that the revised version was substantively different from the one first signed Jan. 27.

Hawaii Attorney General Douglas Chin spoke with reporters Wednesday outside the federal courthouse in Honolulu. The Associated Press

"A reasonable, objective observer – enlightened by the specific historical context, contemporaneous public statements, and specific sequence of events leading to its issuance – would conclude that the Executive Order was issued with a purpose to disfavor a particular religion, in spite of its stated, religiously-neutral purpose," Watson wrote in the 43-page decision.

He scorned the administration's argument that, because the order affected a only fraction of Muslims worldwide, it could not be said to be either a "Muslim ban" – as some critics have contended – or discriminatory.

"The illogic of the Government's contentions is palpable," Watson concluded. "The notion that one can demonstrate animus toward any group of people only by targeting all of them at once is fundamentally flawed."

Hawaii, which brought the lawsuit, was the first state to challenge the president's new travel ban. It was joined by a local imam whose mother-in-law lives in Syria and would have potentially been barred from traveling to the U.S. by the new order.

Watson's references in his ruling to remarks by Trump and his associates were notable. The judge highlighted Trump's call, in the wake of the December 2015 shooting in San Bernardino, California, for a "total and complete shutdown of Muslims entering the United States until our country's representatives can figure out what is going on."

He also cited Trump associate and former New York City Mayor Rudy Giuliani's statements to Fox News in January, two days after the original order was signed, that when the president "first announced it, he said, 'Muslim ban.' He called me up. He said, 'Put a commission together. Show me the right way to do it legally.'"

And Watson drew from senior adviser Stephen Miller's remarks at a town hall-style meeting in Florida on Feb. 21 that, with what was then the upcoming revision to the travel ban, you're still going to have the same basic policy outcome."