The administration also narrowly interpreted which refugees will be allowed into the country, saying that links with refugee resettlement agencies would not be enough to win them admittance, likely sharply limiting the number of refugees allowed entry in coming months.
The Trump administration's temporary travel ban will go into effect at 8 pm EDT (0000 GMT Friday), but in a scaled-back form that still allows in some travellers from Iran, Libya, Somalia, Sudan, Syria and Yemen, following a Supreme Court order on Monday.
The Supreme Court exempted travellers and refugees with a "bona fide relationship" with a person or entity in the United States from the ban, which Trump signed in March and which opponents have said is discriminatory.
Refugee resettlement agencies had expected that their formal links with refugees expecting to come to the United States would qualify as "bona fide." But US officials said on Thursday that for now, that sort of relationship was not enough to qualify refugees for entry.
The administration's decision likely means that few refugees beyond a 50,000-cap set by Trump will be allowed into the country this year. A US official said that as of Wednesday evening, 49,009 refugees had been allowed into the country this fiscal year. The State Department said refugees scheduled to arrive through July 6 could still enter.
The US government expects "things to run smoothly" and "business as usual" at US ports of entry, a senior U.S. official told reporters.
Trump first announced a temporary travel ban on Jan. 27, calling it a counterterrorism measure to allow time to develop better security vetting. The order caused chaos at airports as officials scrambled to enforce it and was blocked by federal courts, with opponents arguing the measure discriminated against Muslims and that there was no security rationale for it.
A revised version of the ban, issued on March 6, was also halted by courts.
In its decision on Monday, the Supreme Court allowed the ban, which bars people from the designated six countries for 90 days and refugees for 120 days, to go partially into effect until the top court can take up the case during its next term starting in October.
It defined a close familial relationship as being a parent, spouse, child, adult son or daughter, son-in-law, daughter-in-law or sibling, including step-siblings and other step-family relations.
"Grandparents, grandchildren, aunts, uncles, nieces, nephews, cousins, brothers-laws and sisters-in-law, fiancés, and any other 'extended' family members," are not considered close family, according to the cable.
Asked how barring grandparents or grandchildren makes the United States safer, a senior US official did not directly answer, instead pointing to Trump's guidance to pause "certain travel while we review our security posture."
The guidelines also said that workers with an offer of employment from a company in the United States or a lecturer addressing U.S. audiences would be exempt from the ban, but someone who simply made a hotel reservation would not be considered as having a bona fide relationship.
Immigration lawyers expressed surprise and dismay that fiancés, grandparents and grandchildren would not qualify as close family.
Refugee groups also rejected as too narrow the administration's interpretation of the Supreme Court order.
"We're surprised by this interpretation, we thought it would be more favorable, it's not and we're going to question it," said Chris George, executive director of IRIS - Integrated Refugee and Immigrant Services, a refugee resettlement agency.
(Reporting by Yeganeh Torbati and Mica Rosenberg; additional reporting by Arshad Mohammed and Susan Heavey in Washington and Gabriella Borter in New York; editing by Jonathan Oatis and Grant McCool)