The Division's Indian Resources Section also litigates on behalf of federal agencies when they are protecting the rights and resources of federally recognized Indian tribes and their members. This includes both defending against challenges to statutes and agency action designed to protect tribal interests and bringing suits on behalf of federal agencies to protect tribal rights and natural resources. The rights and resources typically at issue include water rights, the ability to acquire reservation land, hunting and fishing rights, and other natural resources.

The Division's Natural Resources Section also defends the implementation of the native American affairs program in federal district courts and the United States Court of Federal Claims, in particular when challenges are brought by Tribes, individual native Americans, or allottees.  The subject matter includes diverse areas, including Indian gaming, tribal recognition, Indian assistance programs, actions with respect to tribal self-government, tribal membership disputes, the management of fiscal and natural resources, as well as cultural and religious issues. The Section defends the United States and its agencies against claims that the United States has not complied with responsibilities to native Americans.  The main federal agency that the Division represents in connection with this work is the Bureau of Indian Affairs.