The commission began as the Bureau of Non-Christian Tribes created by the Insular Government during the American Colonial Period of the Philippines.

In 1972, then President Ferdinand Marcos split CNI into the Southern Philippine Development Authority (SPDA) and the Presidential Assistance on National Minorities (PANAMIN).

[3] The NCIP was under the supervision of the Department of Social Welfare and Development until 2024, when it was transferred to the Office of the President of the Philippines through Executive Order No.

The head commissioner continues to govern the commission, along with the provincial officer, despite the status quo, surging to further criticisms.

Provincial officer of NCIP Oriental Mindoro Karen Ignacio and Puerto Galera mayor Hubbert Dolor retaliated by using the IPRA Law as defense for the establishment of the landfill against the indigenous Mangyan people.

[6] On May 27, 2019, it was later revealed that the NCIP already released a certificate for the company to continue with the destructive Chico river dam project, mounting to indigenous protests.