Like most of Asia's wildlife sanctuaries, Khao Yai has been long under threat from poachers who are stripping the forest of its plant and animal wealth. In March 2000 the government launched the so-called Khao Yai Conservation Project, so hopefully future generations are able to visit this outstanding piece of nature. The park has over 50 km hiking trails, many of them formed by wildlife movement. Elevations range from 100 to 1400 meters.

During the civil unrest in Cambodia during the 1980s and 1990s, the east half of the area suffered from incursions which have been recently reduced, although there remains unexploded ordinances on the border of the Ta Phraya Park . Settlers and insurgents have cleared land for farming which has now become grassland and secondary woodland. They have hunted the larger mammals and have aided in depleting its wildlife. There are still problems of encroachment by farms, buildings, highways, habitat degradation and disturbance, illegal sport hunting and poaching, illegal logging and the harvesting of forest products like aloe wood. In the east there is encroachment for agriculture, in the west for the development of resorts and estates. In the past this has led the Parks’ administrations to emphasize law enforcement.

Coordination between park staffs is not always smooth, and due to inadequate funding the staff cannot spend enough time on relations with the public. Management is made more difficult by the complicated boundaries of the complex, especially in north and northwest Thap Lan where the most significant incursions and farmland clearances have occurred; also in most of Ta Phraya which has an equally high ratio of boundary to area, making protection of the remaining linear stretch of forest along the Thai-Cambodian border difficult. There is no clear external buffer zone delineation and other land uses border directly onto protected areas. Except where the northern boundary of Thap Lan borders the Sakaraet Biosphere Reserve.

The Government is committed to boundary adjustments by 2007. This will result in the degazetting of 437.73km² of inhabited degraded land in Thap Lan and the addition of 176.27km² of primary forest from the National Forest Reserve. Fragmentation of the area by roads is another ongoing threat. Highway 304 to Korat separates Khao Yai from Thap Lan along a strip of agricultural land. A highway runs north within a 100m-wide clearing from Prachinburi through western Khao Yai, and a highway crosses the west end of Ta Phraya and between the two sections of Dong-Yai. Although speed humps have been introduced in Khao Yai in an attempt to enforce speed limits, road deaths occur on all three roads since they cross wildlife corridors which should remain continuous if the complex is to realize its potential as a reserve. To overcome this fragmentation, the construction of underpasses and green overpasses has been considered. In 2004 the Thai Government approved a budgetary allocation to undertake a feasibility study for construction of wildlife corridors.

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