WASHINGTON — John F. Kelly, the secretary of the Department of Homeland Security, eased a key part of President Trump’s immigration order on Sunday, saying that people from the affected countries who hold green cards will not be prevented from returning to the United States.
“In applying the provisions of the president’s executive order, I hereby deem the entry of lawful permanent residents to be in the national interest,” Mr. Kelly said in a statement. “Accordingly, absent the receipt of significant derogatory information indicating a serious threat to public safety and welfare, lawful permanent resident status will be a dispositive factor in our case-by-case determinations.”
Even with his statement, much of the order was still being enforced, and travel was disrupted for many around the world. Thousands of protesters gathered for a second day at American airports and other public spaces amid uncertainty about whether federal officers were fully complying with court orders blocking the immediate deportation of some people arriving from affected countries and requiring that anyone detained be granted access to lawyers.
With thousands of protesters marching outside the White House and thronging the streets of Washington and other cities, Mr. Trump late Sunday defended his order. “To be clear, this is not a Muslim ban, as the media is falsely reporting,” he said in a written statement. “This is not about religion — this is about terror and keeping our country safe.”
He noted that the seven countries singled out were identified by former President Barack Obama’s administration as sources of terrorism and that his order does not affect citizens from dozens of other predominantly Muslim countries. “We will again be issuing visas to all countries once we are sure we have reviewed and implemented the most secure policies over the next 90 days,” he said.
As for Syria, whose refugees he has banned indefinitely, Mr. Trump said he was mindful of the suffering of victims of the long-running civil war. “I have tremendous feeling for the people involved in this horrific humanitarian crisis in Syria,” he said. “My first priority will always be to protect and serve our country, but as president I will find ways to help all those who are suffering.”
While Mr. Trump denied that his action was targeted against Muslims, just hours earlier he made clear on Twitter that he was concerned about Christian refugees. Part of his order gives preferential treatment to Christians who try to enter the United States from majority-Muslim countries.
In his Twitter post on Sunday morning, Mr. Trump deplored the killing of Christians in the Middle East without noting the killings of Muslims, who have been killed in vastly greater numbers in Iraq, Syria and elsewhere.
Mr. Trump asserted last week that Christians had been “treated horribly” under previous administrations. “If you were a Muslim, you could come in, but if you were a Christian, it was almost impossible,” he said Friday in an interview with the Christian Broadcasting Network. “I thought it was very, very unfair. So we are going to help them.”
In a second Twitter message on Sunday, the president said that the United States needed strong borders and “extreme vetting” to protect itself from terrorists. He cited Europe and “indeed, the world” as evidence that the United States must shut its borders to potential threats.
The president’s order, enacted with the stroke of a pen at 4:42 p.m. Eastern on Friday, suspended entry of all refugees to the United States for 120 days, barred Syrian refugees indefinitely and blocked entry into the United States for 90 days for citizens of seven predominantly Muslim countries: Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen.
A series of rulings by federal judges across the country blocked part of the president’s actions, preventing the government from deporting some travelers who found themselves ensnared by the presidential order. But the court decisions largely stopped short of letting them into the country or issuing a broader ruling on the constitutionality of Mr. Trump’s actions.
Lawyers for those denied entry said on Sunday that there was significant confusion and disagreement among border agents about who was affected by Mr. Trump’s order.
In a statement Sunday morning, the Department of Homeland Security said that agents would “continue to enforce all of President Trump’s executive orders,” and that “prohibited travel will remain prohibited.” But it also said that the department “will comply with judicial orders.”
The legal battles over the president’s order intensified as lawyers for those detained accused the government of failing to abide by the Saturday night rulings and said agents were refusing to allow them access to potential clients, in direct violation of those rulings.
On Saturday, Judge Leonie M. Brinkema of Federal District Court in Alexandria, Va., ordered government officials to “permit lawyers access to all legal permanent residents being detained at Dulles International Airport.” The ruling was one of at least four around the nation temporarily blocking aspects of Mr. Trump’s executive order.
“We continue to face Border Patrol noncompliance and chaos,” said Marielena Hincapié, the executive director of the National Immigration Law Center.
Lawyers gathered on Sunday morning at Dulles International Airport said that border agents had told lawyers that they would not be permitted to see anyone who was being held. Sharifa Abbasi, 32, one of the lawyers, said a customs agent had told her that “upper management” had instructed agents at Dulles not to provide any information or access to lawyers at the airport.
By Sunday afternoon, lawyers at Dulles were considering seeking a contempt order from Judge Brinkema against the border agency.
In New York, lawyers for the American Civil Liberties Union filed a request for clarification with the Brooklyn judge who had blocked part of the president’s order Saturday night.
“Petitioners’ counsel have received repeated reports of individual members subject to the order who have been placed on planes, possibly deported,” the lawyers wrote in a motion to the court.
The confusion in enforcing the president’s order was particularly evident in the handling of those who have valid green cards, making them legal permanent residents of the United States.
On Saturday night, the Department of Homeland Security said that Mr. Trump’s order did apply to green card holders who were traveling to the United States from the seven countries affected.
White House officials reiterated that position in a briefing for reporters on Saturday afternoon, saying that green card holders from the seven countries would need a case-by-case waiver to return.
Reince Priebus, the White House chief of staff, appeared to change that position Sunday morning. “As far as green card holders, moving forward, it doesn’t affect them,” he said on NBC’s “Meet the Press” program.
He defended Mr. Trump’s order, saying it had been carried out smoothly and was protecting Americans from terrorist threats. On Saturday, a day after the order was issued, airports were marked by scenes of confusion and protest as officials tried to interpret the order, including how to handle green card holders.
Around the globe on Saturday, legal residents of the United States who hold valid green cards and approved visas were blocked from boarding planes overseas or detained for hours in American airports.
Mr. Priebus said several times during the NBC interview that green card holders would not be subject to the order “going forward.” But he repeatedly suggested that anyone, including American citizens, who traveled from any of the seven predominantly Muslim countries identified in the order would be subjected to additional scrutiny.
“If you’re an American citizen traveling back and forth to Libya, you are likely to be subjected to further questioning when you come into an airport,” Mr. Priebus said. He added later, “There is discretionary authority that a customs and border patrol agent has when they suspect that someone is up to no good when they travel back and forth to Libya or Yemen.”
Mr. Priebus said that travelers from the seven countries would be “subjected, temporarily, with more questioning, until a better system is put in place.”
Mr. Trump — in office just a week — has found himself accused of constitutional and legal overreach with his executive order. Large crowds of protesters turned out at airports around the country to denounce Mr. Trump’s ban.
Lawyers who sued the government to block the White House order said the judge’s decision could affect an estimated 100 to 200 people who were detained upon arrival at American airports.
Judge Ann M. Donnelly of Federal District Court in Brooklyn, who was nominated by former President Barack Obama, ruled just before 9 p.m. Saturday that carrying out Mr. Trump’s order by sending the travelers home could cause them “irreparable harm.” She said the government was “enjoined and restrained from, in any manner and by any means, removing individuals” who had arrived in the United States with valid visas or refugee status.
The ruling does not appear to force the administration to let in people otherwise blocked by Mr. Trump’s order who have not yet traveled to the United States.
The judge’s one-page ruling came swiftly after lawyers for the American Civil Liberties Union testified in her courtroom that one of the people detained at an airport was being put on a plane to be deported back to Syria at that very moment.
Hundreds of people waited outside the courthouse chanting “Set them free!” as lawyers made their case. When the crowd learned that Judge Donnelly had ruled in favor of the plaintiffs, a rousing cheer went up in the crowd.
Minutes after the judge’s ruling in New York, another judge, Leonie M. Brinkema of Federal District Court in Virginia, issued a temporary restraining order for a week to block the removal of any green card holders being detained at Dulles International Airport.
Throughout the day on Saturday, there were numerous reports of students attending American universities who were blocked from returning to the United States from visits abroad. One student said in a Twitter post that he would be unable to study at Yale. Another who attends the Massachusetts Institute of Technology was refused permission to board a plane. A Sudanese graduate student at Stanford University was blocked for hours from entering the country.
Human rights groups reported that legal permanent residents of the United States who hold green cards were being stopped in foreign airports as they sought to return from funerals, vacations or study abroad.
The White House said the restrictions would protect “the United States from foreign nationals entering from countries compromised by terrorism” and allow the administration time to put in place “a more rigorous vetting process.” But critics condemned Mr. Trump over the collateral damage on people who had no sinister intentions in trying to come to the United States.
White House aides said on Saturday that there had been consultations with State Department and homeland security officials about carrying out the order. “Everyone who needed to know was informed,” one aide said.
But that assertion was denied by multiple officials with knowledge of the interactions, including two officials at the State Department. Leaders of Customs and Border Protection and of Citizenship and Immigration Services — the two agencies most directly affected by the order — were on a telephone briefing on the new policy even as Mr. Trump signed it on Friday, two officials said.