After the creation of NIA under RA 3601 in June 22, 1963, there was only one Regional Center. Later on, two Regional Offices were created: Region 7 located at Molave, Zamboanga del Sur and South Cotabato. However, with the new regionalization scheme for the island of Mindanao (MC No. 12 s. 1978), jurisdiction over the Provinces of Zamboanga del Norte, Zamboanga del Sur, and Sulu Archipelago was transferred to Region 7, now called Region IX with headquarters in Zamboanga City.
In the succeeding years, an Executive Order No. 429 dated October 12, 1990 was issued and duly signed by Her Excellency Corazon C. Aquino stating that City of Pagadian shall serve as the Regional Center whereas the City of Zamboanga shall remain as the commercial and industrial center.With this, NIA Region IX Regional Office is presently located in Pagadian City wherein transfer of employees were made in two batches dated March 24, 2008 and August 19, 2008.