But Tuesday's order would prevent travellers from Guinea, Liberia or Sierra Leone from transferring to flights to other US airports where they would not necessarily have to pass additional screening.
"If not already handled by the airlines, the few impacted travellers should contact the airlines for rebooking, as needed," Homeland Security Secretary Jeh Johnson said.
"We currently have in place measures to identify and screen anyone at all land, sea and air ports of entry into the United States who we have reason to believe has been present in Liberia, Sierra Leone or Guinea in the preceding 21 days."
The virus has killed more than 4500 people in West Africa this year, and stoked fears that it could spread beyond the three worst hit countries and become a global threat.
But small outbreaks in Senegal and Nigeria have been halted and, with no new confirmed infections in the United States for six days, authorities are hopeful they have now contained the danger.
- AAP