Mountain tapirs have been completely eliminated from western Venezuela and northern Columbia but still inhabit Ecuador and southern Columbia. More than half of the forests in these regions have been destroyed between 1980 and 1989 and is habitat destruction is continuing even in national parks. Another problem facing mountain tapirs is illegal poaching by local hunters. They are hunted for their meat as well as for their hooves and snouts, which are used as folk cures for epilepsy and heart ailments. The intestines are also eaten and are believed to help prevent infection by parasites.
Hunters are able to obtain high prices for tapir products, accelerating the rate of their decline.
Mountain tapirs are sensitive to habitat disturbances and will disappear within a short time after cattle invade their territories and pollute their waters. Because they can only live in moist, humid ecosystems, these kinds of disturbances result in jeopardizing the existence of this critically endangered species. Another major cause of the decreasing numbers of mountain tapirs is due to the destruction of forest habitats in the Amazon Basin of Ecuador. There have also been suggestions that these two species are mating and hybridizing. In order to protect mountain tapirs it is essential to protect large portions of intact habitat.