The Supreme Court on Thursday allowed the Trump administration to end humanitarian protections that have permitted hundreds of thousands of people from Haiti and Syria to live and work legally in the United States.

President Trump has pushed to terminate the program, known as Temporary Protected Status, as part of his broader crack down on immigration. The program was created by Congress with bipartisan support in 1990 to provide temporary legal status to people whose home countries were deemed unsafe because of war, natural disasters or other crises.

The court’s 6-to-3 decision on Thursday, divided along ideological lines, clears a path for the potential deportation of 350,000 Haitians and 6,100 Syrians, and it is likely to have implications for T.P.S. holders from about a dozen other countries.

The three liberal justices dissented.

Since Mr. Trump returned to office last year, his administration has attempted to end T.P.S. for people from 13 out of 17 countries with the designation when President Joseph R. Biden Jr. left office. The administration has separately halted the resettlement of refugees and has dramatically slowed the consideration of asylum claims. The changes collectively have made it far more difficult for people who come from troubled or war-torn nations to find refuge in the United States.

The homeland security secretary determines when T.P.S. should be available to migrants from any specific country, and the designation can last from six to 18 months. There is no limit to how many times a designation for a particular country can be extended.

The law allows the secretary to periodically review such protections, terminating or extending them for certain countries. But the law requires the secretary to consult with relevant federal agencies, including the State Department, about conditions in a country and then make a decision based on those assessments before initiating a change.

The program had been repeatedly extended, becoming all but permanent for recipients from Haiti, Syria and several other nations where crises have spanned many years. Last year, Kristi Noem, the homeland security secretary at the time, moved to withdraw the protections from various countries.

Both sides in the case before the court agreed that the law allows the administration to periodically remove countries from the T.P.S. program and that once terminated, beneficiaries lose legal protections and have to leave the United States.

But immigrant rights advocates said Homeland Security Department officials failed to properly assess country conditions as required by the law. In the case of Haitians, they said the administration was motivated by anti-Black and anti-Haitian prejudice in violation of constitutional prohibitions against discriminatory government actions.

Class-action lawsuits were filed by T.P.S. holders, including engineers, students, doctors and caregivers, who want to continue to work and live in the United States because, their lawyers say, they could be killed if they were forced to return to Syria or Haiti.

During oral arguments in April, the court’s liberal justices pressed the administration’s lawyer about whether the decision to end the program for Haitians was racially motivated. The justices cited the president’s false accusations during the 2024 campaign that Haitians in Springfield, Ohio, ate their neighbors’ pets and Mr. Trump’s comments in December about Haitian immigrants being undesirable because they come from a “filthy, dirty, disgusting” country.

D. John Sauer, the solicitor general, said those statements were “unilluminating” and were references to poverty and crime rather than race. Federal law, he said, makes clear that courts cannot second-guess the government’s decision to extend or to end the protections.

The text of the statute prohibits “judicial review of any determination” of the secretary “with respect to the designation, or termination or extension of a designation.”

Lower court judges, however, sided with the Haitians and Syrians, finding that the secretary’s process was subject to court review and that her decisions had been preordained and not based on meaningful analysis. The judges postponed the terminations, prompting the government’s lawyers to ask the Supreme Court to intervene.

The justices fast-tracked the two cases, scheduling them for the final day of arguments for the term.

In a separate case, the Supreme Court last year allowed the Trump administration to move forward with its plans to lift protections for more than 300,000 Venezuelans who had been living in the United States. The justices ruled twice in that case in emergency orders, providing technically temporary authorization to revoke the protected status while the case went through the courts.