The Trump administration's travel restrictions blocking foreigners from six Muslim-majority countries and refugees fleeing persecution will take effect Thursday, following the Supreme Court’s decision earlier this week to temporarily uphold portions of the ban.

David Lapan, a Department of Homeland Security spokesperson, confirmed to NBC News Wednesday evening that the order "will begin to be implemented tomorrow and detailed guidance will be provided to DHS professionals."

A senior administration official told NBC News that it's likely the ban won't go into effect until the evening.

The high court's ruling allowed President Donald Trump to place a 90-day ban on foreign travelers from six countries — Iran, Syria, Sudan, Somalia, Libya and Yemen — as well as a 120-day ban on refugees fleeing persecution from any country when they have no "bona fide relationship" with an entity or person in the United States. The Supreme Court has granted full review of the travel ban and oral argument is set for October.

Related: Supreme Court Reinstates Much of Trump's Travel Ban, Will Hear Case in Fall

At least one Supreme Court Justice was skeptical that a temporary solution was workable. Justice Clarence Thomas in his dissent said that the Court’s “compromise” would “invite a flood of litigation until this case is finally resolved on the merits, as parties and courts struggle to determine what exactly constitutes a bona fide relationship.”

While it’s not clear how many travelers could be affected by the ban, State Department data suggests many if not most foreign travelers to this country have family connections in the United States.

For instance, of the 12,998 immigrant visas issued from Yemen last year, nearly all of the recipients — 12,563 — had immediate family in the United States.

Plans Are Still in Flux

But just how broadly or narrowly federal agencies charged with implementing the Supreme Court’s order will write the guidelines remains to be seen. Both DHS and the State Department had said they were waiting on the Department of Justice to clarify the Court's decision and have largely remained mum on what the new guidelines may entail.

DHS did issue a statement in the immediate aftermath of the Court’s decision, asserting that the Executive Order “will be done professionally, with clear and sufficient public notice, particularly to potentially affected travelers, and in coordination with partners in the travel industry.”

Heather Nauert, a State Department spokeswoman, told reporters on Tuesday that the guidance was still “in flux.”

“People here are hard at work with Department of Justice, and also, I believe, Homeland Security, to try to figure out exactly what this term 'bona fide' should mean and will mean, and then we’ll get that information out to our folks across the world,” she said.

Related: Who Will Be Affected by the Supreme Court's Travel Ban Ruling?

Most visa screenings are done by U.S. consular offices in the applicants’ home countries. The Trump administration already has stated that its revised order would not apply to those with existing visas. Rather, the ban would only bar applications for new visas.

But immigration experts worry that airlines and border agents may not be adequately prepared to enforce the Supreme Court’s decision reinstating a portion of the ban, potentially leaving foreign travelers in the lurch.

Demonstrators from Syria protest at Los Angeles International Airport on February 4, 2017. MIKE NELSON / EPA

Immigrant Advocates Worry About Repeat of Travel Ban Chaos

"It's very hard to make sure everyone reads the rule and applies the rule consistently," said Greg Chen, an attorney with the American Immigration Lawyers Association.

He added that, even for those border patrol agents operating in good faith, they can "read a piece of paper and draw different conclusions."

Advocacy groups say they are lawyering up in anticipation that things may go awry.

“Anywhere there are international flights coming into the United States, we’ve been working with attorneys to make sure they’re on call and prepped in case there are illegal detentions at that airport in violation of the Supreme Court order," said Mark Doss, a supervising attorney at the International Refugee Assistance Project, a New York City-based advocacy group.

What Does “Bona Fide Relationship” Mean?

Immigration advocates note that the term “bona fide relationship” is vague and worry that the Trump administration, in issuing new guidelines, will give too much discretion to border patrol agents or consular officers who may inconsistently interpret the Supreme Court’s meaning.

The justices did point to concrete examples of the type of familial relationships that could qualify, such as a spouse or a mother-in-law, and also suggested that those travelers with acceptance letters to American universities or offers of employment with an U.S. company should also be allowed to enter.

Yet Gerald Neuman, co-director of the Human Rights Program at Harvard Law School said whether relatives outside of an immediate family, for example, aunts and cousins, will be allowed to enter is an outstanding question.

“I think there’s going to be a gray area and we’ll see how much disagreement there is about it and how people respond to it,” he said.

A Lack of Transparency

Neuman also said a lack of transparency about how border patrol agents make on-the-spot decisions at airports could further complicate matters.

“It’s very difficult to know what’s happening with people who arrive in airports in non-public areas,” Neuman said.

Despite having a visa, customs and border patrol can still lawfully prevent foreign travelers from entering the country for a range of security and public health related reasons.

Sarah Paoletti, director of the Transnational Legal Clinic at the University of Pennsylvania law school, said, beyond border patrol agents, she fears airlines may refuse to issue tickets if they believe foreign travelers lack a credible tie to the United States.

Related: Trump’s Footloose Foreign Policy Keeps His Own Team Guessing

“How will the airlines and Customs and Border Patrol treat arriving immigrants from any one of these countries?” Paoletti asked. “The airlines don’t know immigration law and are now left to figure out what this all means.”

Advocates point to the chaos that ensued in January after President Trump issued his first travel ban that went into effect while many immigrant travelers were already in the air and bounded for the United States.

This time around, Paoletti thinks that travelers are more likely to face issues at their point of departure, as airlines will have to check if their travel documents meet the requirements for the issuance of a boarding pass.

The Airlines Weigh In

Most U.S. airlines do not even service the countries affected by the ban, said Penny Kozakos, vice president of communications for Airlines for America, a Washington D.C.-based trade organization.

She said carriers simply follow American regulations when making decisions about who can board an inbound flight.

"Airlines carrying inbound passengers to the U.S. are required to ensure that those passengers are properly documented for entry — this includes a passport and a visa, if required," Kozakos wrote in an email. "The Supreme Court decision this week has not changed any U.S. government procedures that airlines follow for inbound international flights."

Meanwhile, British Airways, which services three of the six countries — Libya, Sudan and Iran — said in a statement that it would comply with new requirements from the U.S. government.

"The safety and security of our customers and colleagues is our top priority at all times," BA said. "We will comply with the new requirements from the U.S. Government and our flights will continue to operate as normal."