The Bramble Cay melomys inhabited a small coral island on the Great Barrier Reef, measuring about five hectares (12 acres) and located in the Torres Strait, between Queensland state and Papua New Guinea.
The mammal had not been seen for almost 10 years and was initially pronounced extinct after "exhaustive" conservation efforts failed, according to a report published by the University of Queensland in 2016.
That finding was confirmed by the Australian government on Monday.
The cause of its extinction was "almost certainly ocean inundation" from rising sea levels over the past decade, which had led to "dramatic habitat loss," accord to the 2016 report.
"It's not a decision to take lightly," Geoff Richardson, assistant secretary for environment and energy, told members of the Senate, or upper house of parliament. "When something is listed as extinct it essentially ceases to get any protection."
Several hundred of the rodents were believed to occupy the island in the 1970s. But their population rapidly declined thereafter. By 1992, the population had dropped so sharply that the Queensland state government classified the species as endangered.
Critics of Australia's conservation efforts say the extinction of the melomys highlights the lack of resources for preserving wildlife.
"Bramble Cay melomys' extinction is an absolute tragedy," said Greens party senator Janet Rice, who is chairing a senate inquiry into the country's extinction crisis.
"Labor and Liberal's addiction to coal is the death warrant for many of our other threatened animals," she said, referring to the mining policies of the major political parties.
If temperatures continue to rise, nearly 8% of all species worldwide could become extinct, a 2015 study by the University of Connecticut found. Australia, New Zealand and South America are considered to be at highest risk.
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