NAPCO actively manages particular areas and ecosystems for nature conservation. Marion Downs was the first property in Western Queensland to be registered with the Land for Wildlife network in 2002, with an area on Goldsborough registered in 2004. In 2005, NAPCO signed an agreement with the Queensland Government to protect more than 200 000 ha of environmentally and culturally significant areas. The Mulligan River Nature Refuge, 200 km south-west of Boulia, protects several regional ecosystems not presently conserved or with low representation in national parks or state reserves in Queensland. Within the refuge are habitats suitable for rare and threatened animals including the mulgara, kowari, freckled duck, grey grass wren and dusky hopping mouse, as well as a series of artesian mound springs known for their use by indigenous people, pastoralists and Afghan camel teams.
The Bullen Bullen Nature Refuge was declared in 2008, and lies in the Southern Gulf region, dominated by arid tropical savannas of native grasses, both perennial and annual, as well as a number of scrubs (Dodenia, Acacia and Eremophlia) and eucalpts. Bullen Bullen provides suitable habitat for a number of critically endangered and vulnerable species including the Throughton's sheathtail bat and the purple-necked rock-wallaby as well as a number of reptile species.
The Toko Range Nature Refuge (declared 2009) adjoins the Mulligan River Nature Refuge and ensures complete coverage of the Mulligan River by conservation agreements. The nature refuge protects Toko Gorge, a Wetland of National Significance and has special value due to its diversity and unusual geology.