Australia’s most iconic sea lion colony is now under direct threat after a confirmed case of H5N1 bird flu on Kangaroo Island in South Australia.

Four greater crested terns have tested positive — including one at Seal Bay, a critical breeding site for the endangered Australian sea lion on the island’s southern coastline.

WATCH ABOVE: Bird Flu threatens iconic Kangaroo Island sea lion colony

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About 5 per cent of the species’ entire global population lives at the site and conservation groups say the detection has turned months of warnings into an immediate wildlife emergency.

Experts fear the virus could devastate the already fragile population of just 12,000 animals which are found nowhere else on Earth.

There are fears for the sea lion colony on Kangaroo Island after a bird in Seal Bay tested positive to bird flu. Credit: 7NEWS

H5N1 has already been catastrophic for marine mammals, killing 30,000 sea lion pups in South America in six months and wiping out about 13,000 elephant seal pups on Australia’s remote Heard Island last summer.

Australian Marine Conservation Society campaigns director Alexia Wellbelove says the Seal Bay detection is the moment they hoped would never come.

“This is the news we feared but predicted given the experience of bird flu internationally,” she said.

“Endangered Australian sea lions are now on the frontline of the potential wildlife crisis, and a positive detection in a greater crested tern at one of the largest breeding colonies means we must be on high alert.

“With only 12,000 individuals left, the Australian sea lion simply cannot absorb the kind of losses we have seen bird flu inflict on marine mammals overseas.”

Thousands of elephant seals on Heard Island have died from suspected bird flu. Credit: Australian Antarctic Program

Wellbelove says the threat is now “very real”, with the virus known to jump from birds to seals and sea lions overseas.

“In South America, this virus killed 30,000 sea lion pups in just six months. On our own Heard Island, it killed more than 13,000 elephant seal pups in a single season,” she said.

“With a positive bird flu detection at this important colony, we now have to face the very real possibility of similar devastation here at home, in a species already teetering on the edge.”

The conservation charity says the federal government must immediately establish a $200 million national wildlife resilience fund to protect at‑risk species and respond to emerging threats.

“This is no longer a question of prevention,” Wellbelove said.

“Every colony, every pup, every individual matters when a population is this small. We cannot afford to wait.”

Environmental organisations are now pushing for co-ordinated national action as authorities continue testing and surveillance across Kangaroo Island.