About 30 of the venom-resistant predators were released on Amami Oshima, a UNESCO World Heritage site, in the late 1970s to keep down the population of habu, a pit viper whose bite can be deadly to humans.
However, the snakes are mostly active at night when mongooses prefer to sleep and the toothy mammals turned their ravenous appetites to local Amami rabbits, drastically reducing their numbers.
"It is said that the mongooses, which are active during the day, rarely came into contact with the nocturnal habu snakes," a local official told AFP.
The rabbits only live on Amami Oshima and one other island and are listed as endangered on the International Union for Conservation of Nature (IUCN) red list.
The mongoose population had exploded to around 10,000 by 2000 and Japanese authorities began a programme of eradication that reportedly included specially trained sniffer dogs.
The government declared the island mongoose-free on Tuesday, almost 25 years after the start of that programme and nearly 50 since the ill-fated initiative began.
"(This) is genuinely good news for our prefecture and for conservation of World Natural Heritage site Amami's precious ecosystem," local governor Koichi Shiota said in a statement.
"There are many lessons we should learn from the impact on native ecosystem that mongooses brought, and efforts and costs required for us to eradicate it," he said.
More than 37,000 alien species have taken hold worldwide far from their places of origin, costing upwards of $400 billion a year in damages and lost income, a UN panel said in 2023.
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