Maliau Basin was originally part of a timber concession belonging to Yayasan Sabah (Sabah Foundation), an organization formed in 1966 through an Enactment of the Sabah State Legislative Assembly, with the mission of improving the standard of living and education of Malaysians in Sabah. Recognizing the uniqueness of the area, in 1981 Yayasan Sabah voluntarily designated Maliau Basin as a Conservation Area, for the purposes of research, education and training, along with Danum Valley Conservation Area further to the east.
In 1997, Maliau Basin conservation Area was upgraded by the Sabah state government to a Class 1 Protection Forest Reserve, providing legal status as a protected area, and extended to its present size of 588.4 km2 by incorporating forested land to the eastand north of the Basin. Maliau received further protection in 1999 when it was gazetted as a cultural heritage site under the state Cultural Heritage (Conservation) Enactment. Buffer zones surrounding the whole Conservation Area also add to its protection.
Day to day management of the Conservation Area is carried out by Yayasan Sabah on behalf of an inter-agency Maliau Basin Management Committee, which also includes Sabah Forestry Department, Sabah Ministry of Tourism, Culture and Environment, Universiti Malaysia Sabah and representatives from other government agencies, academic institutions, District Offices and NGOs.
In 1999, a 4-year project was initiated between Yayasan Sabah and DANIDA (Danish International Development Assistance), resulting in the preparation of a Strategic Management Plan for Maliau Basin Conservation Area, and the establishment of Maliau Basin Studies Centre at the southeast edge of the Basin for research, conservation, education and eco-tourism purposes.
Generous sponsorship has come from Swedish company IKEA who funded a vehicle, satellite camps, trail and bridge construction, observation towers and the Maliau 'Sky Bridge' while Sabah Shell Petroleum Limited sponsored the construction of Shell Maliau Basin Reception and Information Building.