Conservationists have made the first physical contact in over four decades with a Sumatran rhino in Indonesian Borneo.

The smallest of the three Asian rhino species, hairy rhino numbers have plummeted to less than 100 due to hunting and habitat loss, with the last wild populations in Kalimantan, Borneo, and the island of Sumatra.

Experts said the capture of a female rhino on 12 March was “outstanding” and “unprecedented”, and marked the first live sighting of one in the area in over 40 years rather than on camera trap or by evidence such as footprints and dung.

“That’s a very, very rare thing,” said Simon Stuart, a rhino expert at the International Union for the Conservation of Nature, who said the dense rainforest and remote nature of the area made sightings difficult. “Finding a single Sumatran rhino is good news given we can’t even account for 100 in the world.”

The female Sumatran rhino, which is estimated to be between four and five years old, was safely captured in a pit trap in Kutai Barat in East Kalimantan on 12 March. Photograph: Ari Wibowo/WWF

“It’s really a very exciting find,” said Glyn Davies, conservation director at WWF-UK, which captured the rhino using a wooden pit in order to protect it. Part of the reason the beasts were so hard to find is they are “very, very secretive,” he said. The rhino have been sighted in Sumatra more recently than in Kalimantan.

Once widespread across south-east Asia, from northern India to southern China, the Sumatran rhino (Dicerorhinus sumatrensis) was declared extinct in the wild in Malaysia last year, making Indonesia their final stronghold. But their low numbers, combined with a lack of international funding and political commitment locally for an action plan led conservationists in 2015 to warn the final ones might go extinct.

The Borneo female will now be re-homed in a sanctuary around 100 miles from where she was captured. Stuart said that because of previous experiences where poachers had arrived weeks after specific locations for Sumatran rhino sightings had been declared, it was important that the location of its new home was kept “really, really vague.”

The first live sighting of a Sumatran rhino in Kalimantan, the Indonesia part of Borneo, in over 40 years. Photograph: Ari Wibowo/WWF

A further 15 Sumatran rhino have been identified in Kalimantan with camera traps, but Stuart and Davies said it was too early to say whether those and the animal captured were enough for a viable breeding population. The female of the species need to breed regularly or can develop tumours that render them infertile.

Last year the only male Sumatran rhino in the western hemisphere was transported on a 55-hour journey from Cincinnati zoo to Sumatra, to help the remaining population to breed.