It is presumed to have similar ecological requirements to M. moluccarum in that it is a lowland species associated with streams, lakes and other waterbodies from which it captures fish, frogs and other prey. It has been found to roost in small numbers in deep crevices and cracks in caves, often with other species (Flannery 1995).

This species has been recorded from the island of Borneo (Sabah), the Indonesian islands of Java, Mendanau, Kangean and Flores (Corbet and Hill 1992, Flannery 1995, Ospina-Garces et al. 2016) 
Records from Vietnam are thought to be referring to misidentified Myotis horsfieldii (Borissenko et al. 2003), while those from Australia refer to M. macropus (Cooper et al. 2001). Records from Sulawesi and satellite islands refer to M. moluccarum and those from New Guinea refer to M. moluccarum and M. macropus (Cooper et al. 2001).

It is not known if this species is present in any protected areas. It is a relatively poorly known species and further studies into its taxonomy, distribution, habitat and ecology, and threats are needed.