President Trump’s revised order Monday to hit the pause button on refugees and visitors from terrorist hotbeds was aimed at erasing the perception that it was a “Muslim ban,” but a new round of court challenges appeared unavoidable.

The latest version dropped Iraq from the countries targeted in the president’s original Jan. 27 executive order, which was blocked by a federal court injunction. Visitors now will be banned for 90 days from six Muslim-majority countries on the list: Iran, Libya, Somalia, Sudan, Syria and Yemen.

During the ban, the administration plans to develop an extreme vetting program for all foreign visitors to the U.S., including a biometric entry/exit system to identify who is arriving and departing the country.

It also removed the original order’s exemptions for religious minorities, namely Christians, from the targeted countries, and it eliminated a permanent ban on refugees from Syria.

The order supported the designation of terrorist-threat countries, which were previously identified by the Obama administration, by noting the absence of a functioning or reliable government to provide reliable information about travelers, underscoring that Muslims were not targeted.

The 90-day ban on visitors and the 120-day halt to refugee resettlement this time will phase in over a 10-day period, taking full effect March 16.

The administration hoped to avoid the chaos that occurred when they sprang the original order on the public in January, when travelers were caught by surprise in transit, with some detained at airports and others sent back to their home countries.

When the new order takes effect, it will revoke the first order now tied up in litigation. The tweaks were all designed as a bulwark against lawsuits.

A federal judge in Seattle blocked Mr. Trump’s first stab at a travel ban. A three-judge panel of the 9th U.S. Circuit Court of Appeals in San Francisco unanimously upheld the injunction, saying the order was too broad and the president had exceeded his national security powers to cause unwarranted headaches for citizens, immigrants and their relatives abroad.

Despite taking pains to avoid those pitfalls, Cornell University Law School professor Stephen Yale-Loehr said it was “essentially old wine in a new bottle.”

“The revised executive order will not quell litigation or concerns. U.S. relatives will still sue over the inability of their loved ones to join them in the United States. U.S. companies may sue because they cannot hire needed workers from the six countries. And U.S. universities will worry about the impact of the order on international students’ willingness to attend college in the United States,” said the immigration law scholar.

Indeed, civil liberties groups and state attorneys general who sued over Mr. Trump’s first executive order immediately prepared round two, unconvinced that the new order addressed their constitutional concerns.

Lee Gelernt, deputy director of the American Civil Liberties Union’s Immigrants’ Rights Project, said his organization intends to continue challenging the new executive order and will likely amend its current lawsuit rather than file a new one.

“We believe the core constitutional problem has not been eliminated — which is religious discrimination,” said Mr. Gelernt, who presented the first legal challenge to the executive order in a case brought in New York. “Certain due process problems may be eliminated with the new ban, but the religious discrimination has not been eliminated.”

The Arab American Civil Rights League, which is representing clients in a challenge to the order brought in Michigan, on Monday filed notice that it intends to amend its complaint.

Washington Attorney General Bob Ferguson, who brought the lawsuit that resulted in the nationwide ban on enforcement of the original order, said his office is still reviewing the new order to determine the next legal steps. But he said “the intent behind the original order is a concern to us.”

“That part of our claim is still an area that will especially be focused on in the next few days,” said Mr. Ferguson, referring to additional interviews and research that lawyers in his office plan to conduct in order to learn how Washington businesses, residents, universities and others could be impacted by the new order.

Attorney General Jeff Sessions insisted that the new order, as well as the first, “is a lawful and proper exercise of presidential authority.”

“This Department of Justice will defend and enforce lawful orders of the president consistent with core principles of our Constitution,” Mr. Sessions said at a rollout of the new order, joined by Secretary of State Rex W. Tillerson and Homeland Security Secretary John F. Kelly.

“The executive is empowered under the Constitution and by Congress to make national security judgments and to enforce our immigration policies in order to safeguard the American public,” he said.

He noted that of the 1,000 terrorism-related cases currently under investigation by the FBI, the subjects in 300 investigations are people who entered the U.S. as refugees.

“Terrorism is clearly a danger for America and our people,” Mr. Sessions said.

Unlike the public signing ceremony for the original order, which involved a personal appearance by Mr. Trump at the Pentagon, the president signed the new immigration order at the White House without press coverage.

White House press secretary Sean Spicer said the low-key events kept the focus on “the implementation of it.”

“That’s what we wanted to highlight today — the government getting it done,” he told reporters at the White House.

A key issue in the previous litigation was Mr. Trump’s call during the campaign for a temporary “Muslim ban” until the government figures out how to deal with the threat of Islamist terrorism. He backed off that description and embrace of “extreme vetting” later in the campaign.

Moving to keep his promise to impose an extreme vetting program, the order called for:

• Uniform screening standards for all immigration programs governmentwide;

• A biometric entry-exit system for all targeted travelers entering and departing the U.S.;

• A review by the State Department of all nonimmigrant visa reciprocity agreements to ensure that they are, with respect to each visa classification, truly reciprocal; and

• New restrictions on the Visa Interview Waiver Program and requirements for nonimmigrant visa applicants to undergo in-person interviews.

In an attempt to demonstrate that the order was not based on religion, it removed exemptions for religious minorities from the predominantly Muslim countries covered by the ban.

It also added exemptions for people who currently have visas or legal “green card” status in the U.S., a carveout that was not included in the original order and added to the confusion.

Although religious minority refugee claims will no longer be prioritized, Mr. Gelernt said he is concerned the travel ban as a whole still disfavors Muslims.

“I think the courts will recognize that simply changing the words of the order will not eliminate the religious discrimination,” the ACLU attorney said.

Virginia Attorney General Mark Herring, who also challenged the original order, called it significant that “President Trump has now revoked his original order and apparently exempted all those persons from his revised order.”

“Although the new order appears to be significantly scaled back, it still sends a horrible message to the world, to Muslim-Americans and to minority communities across the country, without any demonstrable benefit to national security,” Mr. Herring said. “We will closely examine this new order to determine its impact, how it may affect our ongoing challenge to the original ban and whether there are any additional steps we need to take to protect Virginia and our residents.”

The inclusion of Iraq in the original ban raised objections from some U.S. military officials and the Iraqi government because of special consideration previously given to Iraqis who aided the U.S. in the war effort, including translators.

The administration said Iraq was removed form the list, despite the presence of Islamic State fighters in the country, because of extra steps the Iraqi government was taking to share information and assist the U.S. in vetting travelers.

“As a result of this increased information sharing, Iraqi citizens are not affected by the Executive Order. Of course, all normal immigration processing requirements continue to apply, including the grounds of inadmissibility that may be applicable,” according to the fact sheet provided by the administration.

In another change from the original order, Syrian refugees will not be subject to a permanent ban.

Upon resumption of the Refugee Admissions Program, the executive order calls for refugee admissions to not exceed 50,000 for fiscal 2017, cutting by more than half the 110,000 refugees projected to be admitted this year under Obama administration guidelines.

Mr. Trump encountered familiar resistance on Capitol Hill.

“This isn’t about keeping America safe. Let’s call it what it is. This ban is a racist and anti-Islamic attempt to divide us up,” tweeted Sen. Bernard Sanders, the Vermont independent who emerged as a leading voice for the left after his 2016 run for the Democratic presidential nomination.

A who’s who of Democratic lawmakers voiced opposition.

Senate Minority Leader Charles E. Schumer demanded the repeal of the new order. “A watered-down ban is still a ban. Despite the administration’s changes, this dangerous executive order makes us less safe, not more, [and] it is mean-spirited and un-American,” the New York Democrat said.

He also joined in criticism that Mr. Trump delayed the new order because of the positive reception for his speech last week to a joint session of Congress.

“Delaying its announcement so the president could bask in the aftermath of his joint address is all the proof Americans need to know that this has absolutely nothing to do with national security,” he said. “Despite their best efforts, I fully expect this executive order to have the same uphill climb in the courts that the previous version had.”

• Dave Boyer contributed to this report.

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