Samoan authorities are working to find out whether three sailors who have since tested positive for Covid-19 got off the ship in Apia over the weekend.
It is one of the few countries in the world yet to have a confirmed case of Covid.
It comes after health officials in nearby American Samoa reported three people on board the Fesco Askold container ship had tested positive for the virus.
There are 17 crew members on the ship, local media report. In accordance with local regulations, all on board required a test before they would be allowed onto the island.
None of the crew have been allowed off the ship since and there are now moves to send it out to open waters.
The ship, however, arrived via Apia - the capital city of what was once known as Western Samoa, but which is now Samoa - the day before.
It spent just over 22 hours docked in Apia, on Sunday (local time) and it remains unknown whether any of the crew got off the ship during that period.
Strict restrictions remain in Samoa
Samoa, which battled a deadly measles epidemic last year, has maintained a state of emergency and strict restrictions on international flights despite not having even one confirmed case of coronavirus.
A total of 83 people in the island nation died of measles last year - most of them young children and babies.
The devastation the country suffered last year is part of the reason current restrictions related to Covid-19 continue; as the country is intent on keeping the deadly virus out.
Samoa's health authorities were alerted to the latest situation regarding the sailors last night, American Samoa's director of health Motusa Tuileama Nua told the Samoa Observer.
"Reconfirmed tests have been positive too," Nua said of the cases.
"The vessel is now being sent out to open waters. We have to figure out what to do with this boat."
All 11 health personnel who carried out tests on the crew, in American Samoa, are now under strict quarantine.
Despite none of the people on board being allowed off the ship, local schools have been alerted and students have been instructed to wear masks, according to the Talanei news site.
Officials in Samoa are yet to comment on the situation.
The ship - under the Cyprus flag - had earlier been in San Francisco and Oakland before heading to Pape'ete in Tahiti, French Polynesia before going to Samoa.