Yet the high court has already allowed a for-profit business, Hobby Lobby, to withhold providing contraceptive coverage to employees under the Affordable Care Act based on the owner's religious beliefs.
The officials say the Yemenis were allowed to board EgyptAir flight 985 to John F. Kennedy airport early on Tuesday because Cairo airport authorities had yet to receive official instructions from the United States on how to implement the ban.
The limited reinstatement of the travel ban is anticipated to take effect on or about June 29, 2017. Critics called it a discriminatory "Muslim ban".
Only the small group of individuals with no connections in the United States can be prohibited from entering the United States under Monday's decision.
In its ruling, the court reminded the Trump administration that its Executive Order was meant to be temporary, allowing for that 90 day review.
The justices will hear arguments in the case in the fall.
The ruling also said it would permit a 120-day ban on all refugees entering the United States to go into effect.
On the other hand, the justices said, relationships created for the purposes of evading the travel ban will not be considered valid.
Justice Clarence Thomas, joined by Samuel Alito and Neil Gorsuch, said the government has shown it is likely to succeed on the merits of the case, and that it will suffer irreparable harm with any interference. Refugees from these countries would be denied entry for a period of 120 days.
The U.S. Supreme Court agreed to reinstate much of President Trump's travel ban the lower courts had previously blocked.
"My number one responsibility as Commander in Chief is to keep the American people safe". However, I'm particularly concerned that banning people from the United States due to their country of origin sends a chilling message to all global students that we are not a welcoming place.
Now the administration has a chance to prove to the justices that it can implement the partial ban in an even-handed and orderly way as it argues to restore its full reach and potentially make elements of it permanent.
The court basically said that foreign nationals with no "bona fide relationship" to the United States do not have the same rights and can be barred from entry. "For individuals, a close familial relationship is required", the court said. "I want people who can love the United States and all of its citizens, and who will be hardworking and productive", Trump added.
An official with a higher-education association who asked to remain anonymous to speak freely about the ruling said that at first read, it appears "the court basically agrees with us".
In the meantime, the court said it would allow modified versions of the travel and refugee admissions bans to take effect. That court also put a hold on separate aspects of the policy that would keep all refugees out of the United States for 120 days and cut by more than half, from 110,000 to 50,000, the cap on refugees in the current government spending year that ends September 30.
A worker who takes a job with an American company.
The order was, however, blocked by federal judges before going into effect on March 16 as planned. Rather than pursue an appeal, the administration said it would revise the policy.
Some lawyers also said the vagueness of the "bona fide" standard was license for the Trump administration to interpret it broadly.
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