Five Iraqis and a Yemeni national arrived at Cairo airport to board an Egyptair flight bound for the JF Kennedy Airport in NY, the sources added.
Hussein, who is responsible for EgyptAir's daily flight to NY, said authorities there had notified them hours earlier of the new restrictions.
EgyptAir representatives did not immediately respond to phone calls, and the airline's website did not provide updated travel advice for the United States.
Egyptian authorities barred six Arab migrants from leaving for the United States on Saturday, sources at Cairo airport said, hours after President Donald Trump suspended his country's refugee admissions programme.
The travel alert said government officials and their immediate family and global organization representatives were exempt from the restrictions. "These are people with valid visas and legitimate refugee claims who have already been determined by the State Department and the Department of Homeland Security to be admissible and to be allowed to enter the USA and now are being unlawfully detained".
A United Nations Refugee Agency spokesperson said it was not yet known whether the six travellers had been granted visas earlier under the USA refugee programme.