Department of Conservation rangers found the long-tailed bats near the Kepler Track Great Walk in Fiordland after automatic recording devices led them to just the second known colony of the creatures in the region.
Doc ranger Warren Simpson said 60 of the critically endangered bats had been observed, and the colony was believed to number about 100.
Long and short-tailed bats are the country's only native land mammals, and both are critically endangered.
In mid-December, Bay of Plenty Polytechnic students recorded hundreds of bat passes on automated recording equipment in the Iris Burn Valley. The "bat boxes" picked up the animal's high-frequency echo-location calls.
The students tipped off rangers and the Fiordland Conservation Trust, which had been looking for the bats near Lake Te Anau.
After relocating to the valley, rangers caught four bats, two of them breeding females.
"We attached a tiny radio transmitter to each female so we could track them down to their maternity roost trees," Mr Simpson said.
"This is when we discovered they were roosting so close to the Kepler Track."
The bats, which can fly at 60kmh, were seen leaving the roost trees in darkness. They then made huge round trips of 20km to feed on insects at their favourite waterways. Their home range can be up to 100sq km.
Five maternity roost trees have now been discovered in the Iris Burn Valley, less than 500m from the Kepler Track.
Doc biodiversity ranger Jo Whitehead said techniques had not been developed to transfer bats to predator-free environments.
Native bats, once plentiful in South Island towns and forests, were decimated by rats during plague years and the clearance of their habitat for development.
The creatures, which breed in large, lofty trees such as silver birch, produce only one offspring a year.
Ms Whitehead said she hoped the find would encourage protection work such as pest control to save the colony.
