Tonga had been one of the few countries to have remained virus-free throughout the pandemic - with just one case recorded - and concerns were raised that aid efforts following last month's disaster risked exposing the island to Covid.
The volcanic eruption and tsunami, which left three people dead in Tonga and two in Peru, tainted drinking water, severed communications and left dozens homeless.
Australia, New Zealand, Japan, the UK and China had promised to drop off supplies of fresh water and medicine without coming into contact with anyone on the ground. Travellers to Tonga are usually required to spend three weeks in quarantine.
But despite the precautions, dozens of sailors aboard the Australian aid ship HMAS Adelaide tested positive, while crew members aboard aid flights from Japan and Australia also reported infections. The two positive cases that prompted the lockdown came after officials tested 50 front-line workers at the port, local news site Matangi Tonga reported.
Since the pandemic began, Tonga had previously reported just a single case of the virus when a missionary returning from Africa tested positive in October after flying home via New Zealand.
Tonga and several other small Pacific nations, including Kiribati and the Solomon Islands, were among the last places on the planet to have avoided any virus outbreaks, thanks to their remote locations and strict border controls.
But that has changed in the last few weeks as their defences appeared no match against the highly contagious Omicron variant.
The lockdown in Tonga comes as many homes and businesses remain without internet access after the tsunami severed the sole fibre-optic cable that connects the country to the rest of the world. Officials are hoping repairs will be completed within a week or two.
About 61% of Tonga’s 105,000 people are fully vaccinated, according to Our World in Data.