The mission for NNEPA is as follows: "With respect to Diné values, to protect human health, land, air and water by developing, implementing and enforcing environmental laws and regulations with a commitment to public participation, sustainability, partnership, and restoration."

The Navajo Environmental Protection Commission was established in 1972.

In 1995, legislation made the Navajo Nation Environmental Protection Agency (NNEPA) a separate regulatory branch of the Navajo Nation government and charged it with protecting human health, welfare, and the environment of the Navajo Nation.

In April 1995, the Navajo Nation Council passed a resolution establishing the NNEPA department and approved adoption of the Navajo Nation Environmental Policy Act. This Act provides guidance for , NNEPA in addition to recognizing that a clean environment contributes to maintaining harmony and balance on the Navajo Nation.