There have been 23 cases of COVID-19 recorded among the crew of HMAS Adelaide, which departed Brisbane on Friday to deliver humanitarian aid to virus-free Tonga.
The Department of Defence confirmed the positive cases and close contacts were isolating as per COVID-safe protocols, adding the ship would continue on to Tonga and arrive off its coast early Wednesday morning.
HMAS Adelaide would fulfil its mission to support the relief effort, with humanitarian and medical supplies, engineering equipment and helicopters on board, the department said in a statement.
"Defence recognises the COVID-free status of Tonga, and will ensure the humanitarian supplies and equipment on board are delivered in a COVID-safe manner," it said.
"The ADF has significant experience conducting COVID-19 safe regional responses, including in Fiji following Tropical Cyclone Yasa, which will help contribute to the success and safety of this response."
HMAS Adelaide has "excellent" medical facilities on board and a 40-bed hospital.
All personnel are fully-vaccinated, with COVID-positive people either displaying mild symptoms or asymptomatic.
Earlier, Defence Minister Peter Dutton said the government was working with Tonga to ensure no threat to the Pacific nation.
"They need the aid desperately but they don't want the risk of COVID," the minister told Sky News.
"We will work through all of that as quickly as we can. We are not going to put the Tongan population at risk."
There are over 600 crew onboard.
Tonga was hit by a massive volcanic eruption and subsequent tsunami earlier this month, which has caused significant damage across the nation.
Mr Dutton said aid has already been sent via C-17 planes and contactless delivery remained an option.
"We are not going to put the Tongan population at risk," he said.
Mr Dutton added it was about balancing the quick delivery of aid to the ravaged nation and not exposing the vulnerable population to COVID-19.
"It may mean the ship is able to dock and we provide that support and then move on from there," he said.
"It may mean that they stand off and wait a number of days but we don't have personnel on the ground, it's a matter of dropping the aid and providing that support."
It's the second aid shipment from Australia where a positive case has turned up, with a C-17 plane turned around mid-flight after someone was diagnosed with COVID-19.
