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.
Reports from Samoa indicated MSC was considering a ban on Samoan seamen because the government had apparently refused to repatriate stranded nationals, unless companies met the costs of repatriation.
However government-owned entity, Samoa Shipping Services, said it handles the placement of seafarers with shipping companies worldwide.
Its CEO called the email leak an act of ''sabotage'' saying it was part of an extended conversation on the repatriation of stranded sailors.
Lautimu'ia Uelese Va'ai said MSC was still hiring Samoan sailors, contrary to rumours.
He said the email circulating now was just part of a longer conversation between management in ironing out and finding the best options.
A repatriation flight from Los Angeles arriving in two weeks was expected to carry the first lot of sailors with the government saying 170 would return before the end of the month.
Hundreds of Samoans work on cruise ships and merchant ships around the world.