The species occurs both in cultivated landscapes and in teak forest plantations (Semiadi and Meijaard 2006), with the highest density thought to occur between Semarang and Surabaya on both sides of the border between the provinces of Central and East Java. Recent data (Semiadi 2008, unpubl data) indicate that near Banjar (West Java) there is a possibility of significant numbers of animals in a fragmented teak forest and mixed local and agricultural forest.

The vegetation in which they occur is dominated by mixed age teak (Tectona grandis) plantations interspersed with lalang grasslands (Imperata cylindrical), brush and patches of secondary forest. This apparently provides an optimum habitat for this species. Javan Warty Pigs are everywhere restricted to elevations below about 800 m. The reasons for this are not known, but it might be due to their being unable to tolerate low temperatures (Blouch 1993). They evidently prefer secondary or disturbed forests, though they are also often found near the coasts in remnant patches of mangrove and swamp forest such as in Pangandaran (West Java) and Cilacap (Central Java). They are rare in the few remaining lowland primary forests, and in areas with high human populations where otherwise suitable habitat is fragmented and surrounded by agricultural land. However, they do feed on crops, making nocturnal raids on fields of corn and cassava and, in common with Sus scrofa, the species is widely persecuted for such depredations (Blouch 1988).

The Javan Warty Pig is endemic to Indonesia. Historically the species was present on Java, Madura Island and Bawean Islands; now the species is very fragmented into small pockets of suitable habitat (Grubb 2005). It is extinct on Madura (Semiadi and Meijaard 2006). Two subspecies are recognized. The nominate form, Sus v. verrucosus, occurs on Java (and formerly Madura) where it is sympatric with Sus scrofa vittatus. The second subspecies, S. v. blouchi is confined to Bawean Island in the Java Sea where it is also sympatric with Sus scrofa vittatus. This species was widespread on Java as recently as 1982 (Semiadi and Meijaard 2006), but is now absent from most of the island, and is surviving only in highly fragmented populations.

Javan warty pigs are poorly represented in existing protected areas. Creation of three new nature reserves and expansion of two existing reserves of importance to the taxon were recommended (Blouch 1993). In addition, surveys of the extent of market hunting should be undertaken with the objective of formulating means to regulate or eliminate the practice, and ecological research and investigation on crop damage should be conducted. Captive animals need to be administered under a properly structured plan for the long term genetic and demographic benefit of the species. 
A captive breeding project of S. v. verrucosus is underway and it is breeding the species successfully. A second breeding program is under development. Breeding is so successful that identification of a suitable release site has become urgent. Very few people on mainland Java, however, would gladly welcome releases of the species in their neighbourhood. Suitable release sites therefore need to be identified in well managed protected areas or offshore islands where no people live.