Judge J. Harvie Wilkinson III, appointed by President Ronald Reagan, recused himself, presumably because the government's lawyer in the case, Jeffrey B. Wall, the acting United States solicitor general, is his son-in-law. Judge Allyson Kay Duncan, appointed by Mr. Bush, also disqualified herself, without giving a reason,
Next Monday, the United States Court of Appeals for the Ninth Circuit, in San Francisco, will hear a separate appeal from another decision blocking aspects of the revised travel ban from the federal judge in Hawaii. That appeal will be heard by a three-judge panel.
In its briefs, the administration said the revised executive order made no reference to religion and should be judged on its own merits. Its purpose, the administration said, was to protect national security.
The challengers responded that the volume and specificity of the comments from Mr. Trump and his advisers could not be ignored.
The revised order, issued in March, sought to address judicial objections to the earlier one, issued in January. The first order, which caused chaos and drew protests at airports around the nation, was blocked in February by the Ninth Circuit.
The new order's 90-day suspension of entry from Iran, Libya, Somalia, Sudan, Syria and Yemen was more limited and subject to case-by-case exceptions. The new order omitted Iraq, which had been listed in the earlier one. It removed a complete ban on Syrian refugees. And it deleted explicit references to religion. Like the earlier order, the new one suspended the nation's refugee program for 120 days and reduced the annual number of refugees to 50,000 from 120,000.
Judge Chuang's ruling blocked the part of the order concerning travel from the six countries.
The administration has argued that presidents have vast constitutional and statutory authority over immigration. A 1972 Supreme Court decision said judges should not second-guess the government's "facially legitimate and bona fide reason" for denying visas.
The challengers responded that religious discrimination required a different analysis, one in which motives mattered.
Mr. Trump's most explicit statements about banning Muslims came during the campaign. In a news release in December 2015, for instance, his campaign said, " Donald J. Trump is calling for a total and complete shutdown of Muslims entering the United States."