The playful carnivorous mammal was already rare in the land-locked Central Asian country, but is now no longer visible in its one known habitat there, a ministry spokesman said.
The Eurasian otter "in Kyrgyzstan is either on the verge of disappearance or has already disappeared", the spokeswoman for the Kyrgyz natural resources ministry told AFP.
The Ilbirs Foundation, which seeks to protect the mammal, on Friday released a report saying "the otter has disappeared" from its sole known habitat, "putting in question the species' existence in Kyrgyzstan".
In Europe, the otter is a protected species. Its population declined sharply in the 20th century but has made a recent comeback in some countries such as Britain.
The Kyrgyz ministry spokeswoman said that around 20 otters were previously known to be living in the country's southern Chong-Alay district that Ilbirs has been monitoring.
But not a single otter had been sighted there in 2023 or 2024, suggesting that they have lost their last remaining habitat in Kyrgyzstan.
The ministry spokeswoman cautioned that to give a final answer, it is "necessary to investigate several waterways on which there is no current information".
"However, we estimate the probability that the otter has survived there as low," she stated.
Kyrgyzstan was previously a crucial breeding zone for the otter in Central Asia, the foundation said, warning of a knock-on effect on otters in nearby countries.
One otter was spotted in southeastern Kazakhstan in late December 2024, and another was seen in Uzbekistan in early 2022, the foundation said.
It called the otter population an indicator of the state of waterways in the region.
Scientists have blamed otters' disappearance on a combination of factors including overfishing, mining near rivers, deforestation, damming rivers and dumping of waste.
Kyrgyz authorities said they were seeking funds to carry out reintroduction projects.
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