Despite its large size and importance for biodiversity, the Cerrado is today poorly represented in Brazil's otherwise extensive protected areas system. The region's image as Brazil's agricultural frontier has meant less political will to establish additional parks and enforce stricter legislation. Only about 111,000 km², or 5.5 percent of the total land area, is currently protected, and only around 28,500 km² (1.4 percent) is conserved in protected areas in IUCN categories I to IV.
The most important protected areas in the Cerrado are the 7,290-km² Nascentes do Parnaíba National Park, the 330 km² Chapada dos Guimarães National Park, the 2,000- km² Serra da Canastra National Park (although only about 720 km² are actually protected), the 1,310-km² Emas National Park and the 840-km² Grande Sertão Veredas National Park. In 2001, a large and valuable area of the Cerrado in the State of Tocantins was protected as the 1,588- km² Jalapão State Park. In recent years, private reserves, established under the Private Natural Heritage Reserve system, have become an important component of biodiversity protection in the Cerrado.
Emas National Park, which is currently threatened by the effects of large-scale agricultural activities that surround it, is the site of a partnership between Conservation International and the non-governmental organizations Oréades, Fundação Emas (FEMAS), Pró-Carnívoros, PEQUI, IBAMA and EMBRAPA, along with a group of universities including University of São Paulo, University of Brasília, University of São Carlos and the University of Goiás, are also part of the partnership. The neighboring municipalities and farming cooperatives and environmental agencies of Goiás, Mato Grosso and Mato Grosso do Sul are also involved in the conservation efforts to protect the landscape that includes important biodiversity and the headwaters of the three major Brazilian river systems that converge near the park.
In Grande Sertão Veredas, which was established in 1989, FUNATURA is working to better manage the protected area and protect it from growing agricultural threats using funds obtained through the first and only debt-for-nature swap ever approved for Brazil.
In the Cerrado, indigenous territories total three times the size of the protected area system, which shows how essential these regions are for biodiversity conservation.
In March 1998, a Regional Priority Setting Workshop for the Cerrado was held in Brasilia. The meeting participants identified 70 conservation priority areas and offered suggestions for immediate action. Participants indicated the use of legislative incentives for preservation of biodiversity and water sources. The workshop also recommended the consolidation of existing parks and reserves to create new protected areas. In addition, it identified the need for more intensive faunal and floral surveys of the region.