The Supreme Court dealt President Trump a partial victory Wednesday in the legal battle over his travel ban, allowing the administration to restore strict limits on refugees that were blocked last week by a federal judge in Hawaii.

The win for Mr. Trump, however, was tempered by the high court’s decision to uphold the same judges’ ruling that exempted grandparents and other relatives of U.S. citizens from the administration’s travel ban on six Muslim-majority countries.

Both decisions are temporary, and the case is headed to the San Francisco-based 9th U.S. Circuit Court of Appeals for a full review.

The administration appealed to the Supreme Court after Judge Derrick Watson ruled last week that refugees on file with U.S. resettlement agencies and grandparents qualify for exemptions from the travel ban for people with “close” relationships to U.S. citizens.

Three of the nine justices on the high court — conservatives Clarence Thomas, Samuel A. Alito Jr. and Neil M. Gorsuch — said they wanted to grant Mr. Trump’s request in full.

Josh Blackman, a law professor at South Texas College of Law, said the refugee issue was the more important part of Wednesday’s decision.

The State Department recently changed its policies and began admitting grandparents as “close” relatives, so the decision’s only effect was to allow the administration to implement its refugee program over the Hawaii judge’s ruling, he said.

“It’s at minimum a partial victory and, at maximum, a big victory because they were already complying with the grandparent policy,” said Mr. Blackman. “This doesn’t mean the policy gets upheld, but it has more merit than the lower courts are giving to it.”

Joseph K. Young, a professor of justice, law and criminology at American University who opposes the travel ban, agreed.

“The Trump administration is the bigger winner as long as pieces of the ban are in place,” he said. “It is an ugly, xenophobic policy that hurts our global universities in so many ways, even though they may be exempt partially, so I am obviously strongly opposed.”

Mr. Trump ordered the travel ban as part of an anti-terrorism effort, targeting refugees and travelers from Iran, Libya, Somalia, Sudan, Syria and Yemen because those countries are terrorist hotbeds and lack proper vetting mechanisms.

Critics said the ban was racist and anti-Muslim and that the targeted countries did not include allies that also spawn terrorists, such as Egypt and Saudi Arabia.

Opponents of the ban celebrated the high court’s confirmation of the grandparent exclusion as “close relatives,” which Judge Watson also granted to uncles, aunts, nieces, nephews and cousins of U.S. citizens.

The Supreme Court ruled in June that the travel ban, which was blocked by the courts for months, could take effect but with an exception for “close relatives.” The Trump administration wanted that to apply only to spouses, children, parents, fiances and fiancees.

Judge Watson also decided that potential refugees whose files have been shared with resettlement agencies in the U.S. are considered to have “close” relationships and must be admitted.

The U.S. already has hit the 50,000 cap that Mr. Trump imposed on refugees this fiscal year.

“Given an inch, the Trump administration has tried to take a mile in implementing the ban. That is cruel, unnecessary, and unlawful. said Omar Jadwat, director of the American Civil Liberties Union’s Immigrants’ Rights Project.

“We are glad that the order requiring the government to recognize grandparents and other close family remains in place, but are deeply concerned about the effect of today’s ruling on thousands of refugees who seek to escape dangerous situations, who have been fully vetted by the United States and whose arrival communities, congregations and organizations in the United States have been preparing for and anticipating,” he said. “We look forward to eradicating the entire Muslim ban, which is unconstitutional and repugnant to our most basic values as a country.”

Justin Cox, a staff attorney at the pro-immigration National Immigration Law Center, said the decision was a victory of “family unity.”

“The Trump administration has been clear about its intention to slam the door on Muslims and refugees however it can,” he said. “The opening provided last month by the Supreme Court was abused by the administration, and we will continue to fight alongside our immigrant and refugee communities and in courtrooms to prevent our plaintiffs’ clients from being shut out of the country they already consider their home.”

The decision in Hawaii followed a pattern of federal court rulings on Mr. Trump’s travel ban, which has been tangled in legal battles since it was first attempted in January.

Judges appointed by Democrats have been almost universally skeptical of the president’s actions, digging behind them to try to spot Mr. Trump’s motives. Republican appointees have been willing to take the executive orders on their face, finding they are similar to actions of past presidents.

The Supreme Court last month cut a middle ground, ruling 9-0 that Mr. Trump did, in fact, use valid, wide-ranging powers to decide who should be excluded from the U.S. But the justices said in cases where a potential traveler has “close” ties to the U.S., either through family or a business or school relationship, the U.S. person’s rights must also be respected.

The court, with only vague guidance, left it to the administration to decide what those close relationships were.

• Alex Swoyer and Stephen Dinan contributed to this report.

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