Almost 1,000 Vietnamese had landed in Hanoi by 11 a.m. from the U.K., Germany and France, where the number of coronavirus cases and deaths have been surging.
Health officials will take medical samples from each passenger before they are transferred to quarantined zones.
Due to a large number, about a hundred arrivals remain waiting as of noon.
Tran Hoai Phuong, director of the Northern Airports Authority, said the number of Vietnamese returning in recent days was higher than usual.
Another 5,700 passengers will enter Vietnam from other Southeast Asian countries Wednesday via 78 flights, most of them to land in HCMC and Hanoi.
Vietnam on Wednesday stopped issuing new visas to all foreigners, except for special cases, to limit contagion.
The country has confirmed 68 Covid-19 cases, with the latest being a 41-year old American man who came to Da Nang on March 14.
The Covid-19 pandemic has spread to 167 countries and territories, killing almost 8,000 people.