A federal judge in Maryland on Thursday issued a second temporary restraining order halting part of President Donald Trump's new travel ban.

U.S. District Judge Theodore Chuang halted a provision in the March 6 executive order that would have largely blocked citizens of six majority Muslim nations – Iran, Libya, Somalia, Sudan, Syria and Yemen – from entering the country for 90 days.

That portion had already been blocked by another federal judge in Hawaii on Wednesday, who also halted a 120-day freeze of the U.S. refugee program hours before the order was set to take effect at 12:01 a.m.

Other components of the executive order, including a reduction in the number of refugees allowed to resettle in the U.S. this fiscal year from 110,000 to 50,000, were allowed to go forward.

Chuang was the first federal judge to hear arguments about stopping the travel ban Wednesday, a day that saw four hearings in three corners of the nation.

The International Refugee Assistance Project and HIAS, a pair of nonprofits that provide outreach, legal and advocacy services for refugees, brought the challenge in Maryland along with a handful of individuals. They argued that the travel restrictions amount to discrimination against Muslims, and that there was little evidence the measures would protect national security as the administration has claimed.

Trump administration attorneys rejected those arguments, repeatedly stating the order was religiously neutral, and asserting that the provisions were a much-needed temporary pause that would allow security officials to review screening procedures, an action they argued was well within the scope of the president's authority. They also contended that the new executive order had been specifically tailored to address the concerns raised about the first version, which was frozen nationwide by a federal court in Seattle on Feb. 3.

As with the case in Hawaii, Judge Chuang drew heavily from comments by Trump and his associates on the campaign trail and after the first order was signed.

Trump's statements in the wake of the San Bernardino, California, shooting in December 2015 calling for at least a temporary ban on Muslims entering the U.S., for example, amounted to "explicit, direct statements" of the president's "animus towards Muslims and intention to impose a ban on Muslims entering the United States," Chuang wrote.

Remarks by top White House advisers, the judge added, undercut the administration's argument that the new order is sufficiently different in this regard, and he expressed reservations about the administration's national security argument.

"The fact that the White House took the highly irregular step of first introducing the travel ban without receiving the input and judgment of the relevant national security agencies strongly suggests that the religious purpose was primary, and the national security purpose, even if legitimate, is a secondary post hoc rationale," Chuang wrote.

Nonetheless, while these factors made him skeptical of the administration's national security argument, he declined to "second-guess the conclusion that national security interests would be served by the travel ban."

"These facts raise legitimate questions whether the travel ban for the Designated Countries is actually warranted," Chuang wrote. "Generally, however, courts should afford deference to national security and foreign policy judgments of the Executive Branch."