Twenty-seven seafarers were among close to 300 passengers on the Friday's flight from New Zealand.
The group are now undergoing the government's mandatory 14-days quarantine.
The seafarers, who had worked for Switzerland-registered Mediterranean Shipping Company (MSC), traveled from Dubai to Auckland to catch the flight home.
Earlier the Samoan government had been accused of abandoning seamen stranded around the world because of the Covid-19 pandemic.