The ecology of Javan Ferret Badger is largely unknown, in part because most museum material outside Indonesia is labelled "Java", without providing further information about aspects such as habitat and altitude (Riffel 1991). Recent information suggests wide habitat use. Riffel's (1991) specimen from Bali was found in a matrix of secondary forest and rubber plantation, with human settlements 2 to 3 km distant, suggesting that this species is not reliant on primary forest. This is corroborated by records from Cipaginti, which comprises a mosaic of crop fields, small wood-lots (mostly introduced species) and villages; the nearest patches of remaining native forest are 1-2 km away, and continuous forest cover is about 5 km (Rode-Margono et al. 2014, E.J. Rode-Margono pers. comm. 2014). A number of the recent lowland records are within highly anthropogenic landscapes. There are also records from deep within old-growth evergreen forest (Brickle 2007, Duckworth et al. 2008). Although there insufficient evidence to determine whether populations can persist indefinitely in deforested landscapes far from extensive native vegetation, it is clear that Javan Ferret Badger routinely lives outside native forest.

It is evidently mostly active by night and on the floor (Duckworth et al. 2008) although animals in zoos climb (Riffel 1991). There are several records of more than one (of adult size) in close proximity although what the relationship is of these animals is not clear (Duckworth et al. 2008).

Javan Ferret Badger is confined to Java (where it is known from scattered localities in West, East and Central) and Bali (omitted from the range in most of the standard sources before 1991). Riffel (1991) mapped the locality records then available, such as specimens from Tassikmalaja [=Tasikmalaya], Tjigombong and Buitenzorg [= Bogor] (in the Natural History Museum, London; per A.V. Abramov pers. comm. 2014). Schreiber et al. (1989) marked a locality record without a name (perhaps the Dieng Plateau) in Central Java, but this was not included by Riffel (1991). Recent records confirm its occurrence in Central Java, at the Baturaden-Purwokerto foothills of Gunung Slamet (G. Semiadi pers. comm. 2014) and at Temanggung - Wonosobo (E. Wilianto pers. comm. 2014), and in the adjacent Special Region of Yogyakarta, at Gunung Merapi and at Kulon Progo (Didik Raharyono per E. Wilianto pers. comm. 2014). There are two subspecies: M. o. orientalis in eastern Java, and M. o. sundaicus in western Java (Long 1992); Balinese and Central Javan material seems not to have been identified to subspecies.

Subsequent to Riffel's (1991) map, there are multiple records from West Java, from Cipaganti (Rode-Margono et al. 2014) at 1,350–1,480 m altitude (Spaan et al. 2014); Gunung Halimun Salak National Park (Suyanto 2003, A. Ario pers. comm. 2014); the Cikaniki area of Gunung Halimun Salak NP (Yoneda et al. 1998a), which lies at about 1,000 m (Eaton et al. 2010); Gunung Gede Pangrango National Park, over 1,360–2,230 m (Brickle 2007, Duckworth et al. 2008, Eaton et al. 2010, A. Ario pers. comm. 2014); Gunung Malabar Protected Forest (A. Ario pers. comm. 2014); Gunung Ciremai National Park (A. Ario pers. comm. 2014, E. Wilianto pers. comm. 2014); Gunung Tilu (E. Wilianto pers. comm. 2014); Kareumbi-Masigit Game Reserve (E. Wilianto pers. comm. 2014); Rancamaya Villages - Bogor (E. Wilianto pers. comm. 2014); and Carita (in 1997; J.D. Pilgrim pers comm. 2014); one seen in trade in Jatinegara, Java, reportedly came from Banten province (Mohammad Zulfikar per Erwin Wilianto pers. comm. 2014). There is also one further record from Bali, from Buyan - Tambling (Erwin Wilianto pers. comm. 2014). These records result from incidental observation, not specific search, and in sum therefore suggest that the species is likely to occur at many localities.

The altitudinal range is probably incompletely known but it occurs down to at least 260 m (Bogor specimen in the Natural History Museum, London; per A.V. Abramov pers. comm. 2014) and up to at least 2,230 m (Gunung Gede Pangrango National Park). Most records are from above 800 m but this, at least in part and perhaps entirely, stems from the distribution of remaining native forest: particularly in areas close to large towns, this is mostly in mountains (Smiet 1992), and so this is where most nature observation takes place (E.J. Rode-Margono pers. comm. 2014).

Javan Ferret Badger's use of habitats from the interior of old-growth forest to agricultural landscapes, in an environment of low levels of hunting in the styles which might catch the species, suggest that there are no significant conservation issues for the species at present. However, more information would allow a more confident assessment. The highest priority is probably to monitor market trade levels; fashions for pets can change very quickly (Nekaris et al. 2013) and there is no information from which to speculate on how populations of this species would respond to focussed trade demand. The species occurs in multiple protected areas, potentially many more than those in which it has yet been documented. Javan Ferret Badger is not listed as a protected species in Indonesia. However, according to Indonesian law, species that are not protected may only be traded domestically or internationally following a harvest and export quota system, and because there is no allotted quota for this species, its trade is illegal (Shepherd 2012). Enforcement efforts to counter trade in non-protected species outside the national quota regulations are, however, rarely enforced. Furthermore, enforcement of regulations in the bird markets in Jakarta is also lacking and illegal trade continues on a daily and open basis (Nijman et al. 2014). It is recommended that enforcement efforts are increased in relation to the ongoing illegal trade of this and other species in the bird markets