In Thailand it is found from 140 to 240 m asl in a variety of habitats including pristine forest and farmland adjacent to forest (S. Bumrungsri pers. comm.). In South Asia, little is known about the habitat and ecology of this species. It is presumably it is found in deciduous forests, coniferous forests, bamboo forests and subtropical mixed forests across the foothills of Himalaya.

This species has been recorded from India (Arunachal Pradesh, Manipur, Mizoram, Nagaland and West Bengal) at an altitude range of 100 to 2,100 m asl (Molur et al. 2002), from Thailand (Nakhon Ratchasima Province, Amphoe Pak Thong Chai, Sakaerat Environmental Research Station), Lao PDR, Cambodia and Viet Nam. Some previous records of Megaerops ecaudatus may actually represent M. niphanae.

This species is present in many protected areas. It is classified as a vermin under Schedule V of the Indian Wildlife (Protection) Act. There is a debate over the taxonomic status of two species of the genus Megaerops, with additional taxonomy, survey, ecological studies needed (Molur et al. 2002).