Lesser Short-tailed Bats are associated with old-growth temperate forest, with large trees available for colonial roosts, abundant epiphytes and deep leaf-litter (Parsons and Toft 2021). Colonial breeding trees per colony number only 20–30 (Sedgeley 2003, 2006; Christie and O’Donnell 2015). These roosts have very specific physical and microhabitat characteristics, which are now very rare in New Zealand forests because of the history of logging (Sedgeley 2003, 2006). The species has been recorded at low numbers in logged forest, shrubland, pine plantations, and farmland in areas adjacent to unlogged old-growth forest (Parsons and Toft 2021). Although the species primarily roosts in tree cavities, there are records of the species using caves for roosting (Parsons and Toft 2021).

Lesser Short-tailed Bats are primarily insectivorous but also consume nectar, pollen, and fruit (Parsons and Toft 2021). Lesser short-tailed bats undergo periods of torpor and seasonal hibernation (Czenze et al. 2016, 2017). The species uses a lek mating system (Toth et al. 2018.). Females annually give birth to a single young (Parsons and Toft 2021).
The species is non-migratory and the colonies have large home ranges (ca 150 km², Christie and O’Donnell 2015).

New Zealand Lesser Short-tailed Bat is endemic to New Zealand where it was once widespread on North Island, South Island and several offshore islands. It now occupies less than 30% of its historical geographic range (C. O'Donnell pers. comm.). The species is currently distributed on North Island in the Omahuta-Puketi Forest, in Northland, and throughout tracts of indigenous forest remnants ranging from Taranaki to East Cape (Parsons and Toft 2021). On South Island, populations are now only known from the Eglinton Valley and Murchison Mountains (R. Jackson pers. comm., Edmonds et al. 2017). Large populations of this species are also present on the offshore islands of Hauturu/Little Barrier Island and Whenua Hou/Codfish Island (Parsons and Toft 2021). Lesser Short-tailed Bats range from close to sea level to the upper altitudinal limits of forest cover (Parsons and Toft 2021).

Mystacina tuberculata is protected by New Zealand's Wildlife Act of 1953. Conservation is occurring using guidance from a national Bat Recovery Plan (Molloy 1995), with ongoing assessments and annual work plans being co-ordinated by the national Bat Recovery Group (O’Donnell 2009). Management includes eradications of introduced predators from offshore islands (rats have already been eliminated from islands containing two large offshore populations), predator control at mainland sites (this is just beginning), habitat protection, trial translocations to new habitats, and general advocacy. This species occurs in a number of protected areas. More research is needed to determine the area of occupancy for the species.

There are three subspecies and five evolutionary significant units (ESUs) recognised by the New Zealand Bat Recovery Group and the New Zealand Department of Conservation (Lloyd 2003a,b). The national (non-IUCN) listings for these populations are as follows (O’Donnell et al. 2018):

• Northern Lesser Short-tailed Bat (Mystacina tuberculata aupourica) – nationally vulnerable
• Central Lesser Short-tailed Bat (Mystacina tuberculata rhyacobia) – declining
• Southern Lesser Short-tailed Bat (Mystacina tuberculata tuberculata) – recovering