President Donald Trump’s executive order banning “entry into the United States” for immigrants from “countries of particular concern” continued to alarm immigrants, confuse advocates and pit the new administration of against those who criticized the measure as un-American.

The order, issued Friday and initially targeting specific Muslim-majority nations, sent shock waves through Muslim communities on Long Island, in New York City and across the country, where many felt unfairly targeted.

“It’s a really terrible situation and I never thought this could come from the United States government,” said Nayyar Imam, a Suffolk police chaplain and president of the Long Island Muslim Alliance, which brings together advocates from different mosques in the region.

Even as the order sought to suspend entry for “nearly all travelers” from Iraq, Syria, Sudan, Iran, Somalia, Libya, and Yemen for a 90-day period, reports of people from other countries being detained were adding to the resulting chaos at ports of entry.

Imam said he knew a Long Island man detained at Kennedy Airport after traveling with his family to Saudi Arabia. The man, whose name Imam would not disclose, lives in Dix Hills, works as an accountant, and has been in the United States for about 15 years.

Imam said the man’s family members can’t understand why he was detained — as he and his wife traveled with legal documentation, are not from countries named in the Trump order, and didn’t go to one of those countries.

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“It feels like this could happen to anyone who is a Muslim,” Imam said. “People in the community are scared. I am scared and I am a citizen and a chaplain . . . Why is this being done to us?”

President Donald Trump and his administration continued to defend his move toward “extreme vetting” as a key policy to protect America from potential terrorists and “ensure that those admitted to this country do not bear hostile attitudes toward it and its founding principles,” as the order states.

Under the edict, the United States is also suspending its international refugee admissions program for 120 days, banning access from war-torn places like Syria. Homeland Security officials said lawful permanent residents — also known as green card holders — would be admitted, although the department would decide on issuing visas “on a case-by-case basis.”

Those who support immigration restrictions, like members of Numbers USA, a group in Washington, D.C., that seeks reduced immigration levels, didn’t see the reason for the fuss.

“It is a temporary pause on immigration from certain countries that had been designated by Congress and the Obama administration as terrorist hot spots,” said Rosemary Jenks, the group’s director of government relations. She dismissed protests as “a well-organized effort” by advocates.

The clash over the policy unfolded Monday amid a backdrop of confusion.

There were conflicting reports on how many people exactly had been detained, what procedures were being followed by Customs and Border Protection agents and whether people from countries not on the list were also being singled out for scrutiny.

President Trump tweeted Monday morning that “Only 109 people out of 325,000 were detained and held for questioning” over the weekend, but immigrant advocates said Monday they continued to learn of other cases and they couldn’t possibly know how many people were turned away after arrival.

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“The world is watching and pushing for the administration to at least make some statements and clarify policy” going forward, said Thanu Yakupitiyage, spokeswoman for the New York Immigration Coalition, an group based in Manhattan that is coordinating some of the advocacy efforts. “Ultimately, we’re pushing to completely reverse these executive orders.”

Camille Mackler, legal initiatives director for the coalition, said her organization knew of 42 individuals who had been released, out of 46 identified by the group by Monday afternoon. Those released included detainees from Iran, Yemen, Iraq, Syria, Sudan, Libya, Saudi Arabia and Senegal. Neither Saudi Arabia nor Senegal were listed for additional scrutiny. Advocates said they knew of two travelers deported back to Sudan and Iran.

By late afternoon, advocates were reporting as many as another nine individuals from a Saudi flight detained at Kennedy. They worried about other travelers who didn’t make it to U.S. soil.

This ban, Mackler said, went beyond restrictions placed under other recent administrations.

“In this case — to have such a blanket ban apply with no empirical evidence or justification for it — is pretty unprecedented. And, also the way the ban was rolled out and the chaos that it has created is pretty unprecedented,” she said.

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Gov. Andrew M. Cuomo established a hotline Sunday for relatives of those on flights from affected countries to seek guidance and be connected with legal experts. A Cuomo spokesman reported Monday that 26 callers had sought that assistance in the first 24 hours.

An Iranian man, who did not give his name but identified himself among those released Monday after being held for about eight hours at Kennedy, said through his son that he was resigned to accept what happened. They were driving to Stamford, Connecticut.

“He’s tired, but that’s how it is. We can’t change anything,” said the son, who declined to give his name.

Even though the number of protesters had fallen to about a dozen at Kennedy by Monday afternoon — after thousands rallied there over the weekend and tens of thousands gathered at Battery Park in lower Manhattan on Sunday — advocates said they remained committed to fighting in the courts.

The small crowd that showed up outside Kennedy’s Terminal 4 Monday afternoon, shouted “New York City is for all. No ban. No wall.” They also chanted “Refugees are welcome here. No hate. No fear” before dispersing.

However, several hundred protesters rallied by early Monday night at Tompkins Square Park in Manhattan’s East Village, and the crowd kept growing. As city politicians spoke against the order, the crowd rose to chants of “Dump Trump.”

While the New York Civil Liberties Union and other allies won a temporary block against the ban in the Eastern District of New York, that action and other suits in California, Massachusetts, Virginia and Washington would seek nothing short of having the order canceled, group officers said.

The NYCLU and its allies, said staff attorney Jordan Wells, would continue to press on “a whole range of claims” to fight what he called an “unconstitutional executive order” violating the country’s obligations on the treatment of immigrants, refugees and asylum seekers as well as existing immigration laws and constitutional protections including “the free exercise of religion,” which restricts the government on not giving preference to any one group “on the basis of religion or national origin.”

With Ivan Pereira