In 1992, Philippine President Fidel Ramos appointed Flavier Secretary of the Department of Health. During his term, he initiated various health programs such as "Lets DOH it", "Yosi Kadiri",Oplan Alís Disease, Kontra Kolera, Stop TB, Araw ng Sangkáp Pinoy, Family Planning and Doctor to the Barrios Program.
In 1992, Philippine President Fidel Ramos appointed Flavier as Secretary of Health. During his time in office, he implemented various health programs such as "Lets DOH it", "Yosi Kadiri", Oplan Alís Disease, Kontra Kolera, Stop TB, Araw ng Sangkáp Pinoy, Family Planning and Doctor to the Barrios Program.