Prime Minister Nguyen Xuan Phuc on Tuesday ordered a temporary halt to all inbound international commercial flights as HCMC reported three locally transmitted cases.
Vietnamese airlines were all set to begin operating 33 weekly flights until mid-January.
According to the Civil Aviation Authority of Vietnam (CAAV), around 30,000 Vietnamese nationals wish to return home from Japan and 15,000 each from South Korea and Taiwan, Vietnam's three largest labor markets.
People seeking to return home now have to contact Vietnamese embassies and fly on 10 humanitarian repatriation flights a month to be operated from the three places. On arrival they will be quarantined at military-run isolation facilities.
Vietnam halted international commercial flights on March 25 to keep out Covid-19, and they are yet to resume.
With its strict quarantine and tracking measures, the country managed to quickly contain outbreaks, allowing it to resume economic activities earlier than much of Asia.
It had gone nearly three months without local transmission, but on Monday a HCMC man tested positive after contracting the virus from his friend, a Vietnam Airlines flight attendant.
The flight attendant contracted the virus while in quarantine and spread it to others during his quarantine at home, Minister of Health Nguyen Thanh Long said in a government statement.
His friend then spread the virus to a nephew and a student of his.
Vietnam has had 1,351 cases so far including 35 deaths.