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On July 9, 2018, President Rodrigo Duterte appointed Pangarungan as secretary with cabinet rank and chairman, National Commission on Muslim Filipinos (NCMF). Under its charter, Republic Act 9997, the commission is tasked to uplift the socio-economic and cultural lives of the approximately 8 million Muslims in the Philippines. Pangarungan's priority agenda was to reform the NCMF long dogged by corruption, ensure a comfortable and affordable annual Hajj (Pilgrimage) to Makkah, Saudi Arabia for thousands of Filipino pilgrims, and led a joint nationwide project with the United Nation Development Program (UNDP) and the Japanese Government in strengthening national and local resilience against violent extremism. Pangarungan launched the project at the Mindanao State University in Marawi City on January 23, 2019 in time with the twin explosions in a cathedral in Jolo, Sulu that killed twenty parishioners and 111 wounded. Three days later, a grenade explosion rocked a mosque in Zamboanga City that killed 2 imams and wounding 4 others. These violent incidents were widely condemned by Muslim and Christian leaders in the country.