Samples from the island returned positive results for the infectious disease in a southern elephant seal and a kelp gull, the Tasmanian government said on Thursday.
It is also the first recorded detection in a marine mammal on Tasmanian territory.
The samples were returned with expeditioners who were pulled from the island's research station via icebreaker Nuyina in early October due to psychosocial risks posed by a potential outbreak.
The island is home to large elephant seal populations close to station buildings.
"Expert assessments predict a high likelihood of a significant mortality event during the upcoming breeding season," the federal environment department said in August.
Elephant seals are particularly susceptible to the H5 strain of bird flu.
Roughly 13,000 elephant seal pups died on fellow sub-Antarctic outpost Heard Island after the strain was first detected there in late 2025.
Southern elephant seals, the largest of the world's seals, are listed as a vulnerable species and breed in dense colonies in spring.
Macquarie Island is considered a conservation success story. It was declared free of pests in 2014 after an intensive eradication process.
As of Wednesday, there have been 706 confirmed bird flu events across Australia since it was first detected in June.
South Australia (330) has recorded the most events, including a mass mortality event involving about 900 crested terns.
Under national protocols, H5 bird flu detections are reported as events rather than individual animal detections.
"As bird flu continues to be detected in Tasmania, members of the public are encouraged to continue reporting sick or dead birds," the state government said.
"Reports play an important role in helping authorities detect and respond to potential cases."
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