The island, which lies about 2300km north of New Zealand, closed its borders when the pandemic began and had previously never recorded a single case of Covid-19.
However, a passenger on a repatriation flight from Christchurch, in New Zealand's South Island, had tested positive, Tu'i'onetoa said in a press conference on Friday.
The person, along with the 214 other passengers, had been isolated and quarantined since their arrival in Tonga on Wednesday.
Seasonal workers and some of Tonga's Olympic team officials who got stuck in New Zealand on their way back from the Olympic Games in August were on the flight, local media reported.
They had been denied permission to enter Tonga for weeks after Covid-19 cases were detected in New Zealand.
Tu'i'onetoa asked Tongan residents to prepare for possible restrictions and get vaccinated.
In Tonga, about 48 per cent of the country's eligible population has received a first vaccine dose, while 31 per cent are fully vaccinated.
New Zealand health officials on Thursday announced two cases in Christchurch, the first in the city in a year.
Another two cases in Christchurch were reported on Friday but the city remains without restrictions as health officials deemed the outbreak "contained."
New Zealand's Ministry of Health said in a statement they were investigating the Tongan case, and added that the person had returned a negative pre-departure test before leaving New Zealand.
AAP with The Project