This case was a man who travelled on a special relocation flight from Christchurch in late October.
The Hunga Tonga-Hunga Ha'apai volcano eruption triggered a tsunami that destroyed villages and resorts and knocked out communications for the South Pacific nation of about 105,000 people. Three people died as a result of the disaster.
In a press conference on Tuesday night, Tonga's Health Minister Saia Piukala said the cases are vaccinated and believed they were infected last week. It is not yet known if the two cases are Omicron or not.
Last week, Australia's navy's largest ship docked in the kingdom despite over 20 people on board testing positive for Covid-19.
At the time Tongan Prime Minister Siaosi Sovaleni said no personnel will be allowed to disembark the HMS Adelaide which arrived in the capital Wednesday night.
Sovaleni said Tonga is more concerned about Covid-19 than the clean-up from the volcanic eruption and tsunami.
As result of the first case back in October, Tonga's main island Tongatapu entered a seven-day lockdown
-Additional reporting by RNZ