In 1992, Philippine President Fidel Ramos appointed Flavier Secretary of the Department of Health. During his term, he initiated various health programs such as Oplan Alís Disease, Kontra Kolera,Stop TB, Araw ng Sangkáp Pinoy, Family Planning and Doctor to the Barrios Program. During his term barangay health workers were organized. He served as Secretary of the Department of Health until 1995. He was regularly rated one of the most popular government officials and his department one of the most effective. He was perhaps the most popular Secretary of Health.
Philippine Senate
In 1995, he ran for senator and won under the Ramos administration ticket and was re-elected to a second term in the 2001 elections, placing second among the 12 winning candidates. As senator, he authored and sponsored several landmark bills including the Traditional Medicine Law, the Social Reform and Poverty Alleviation Act, Philippine Clean Air Act, Indigenous People's Rights Act, Anti-money Laundering Act, Barangay Micro-Business Enterprise, National Service Training Program for Tertiary Students, Dangerous Drugs Act, Plant Variety Protection Act, Philippine Nursing Act, the Tobacco Regulation Act, and the law declaring Eid'l Fitr a national public holiday in the Philippines. When he was senator he had a perfect attendance record during sessions, a fact mentioned in the Senate resolution marking his death, which read in part, "The hard-working legislator registered a perfect attendance during the sessions and was instrumental in the enactment of landmark legislations promoting public health care and improving the quality of life of the people." He was also the "poorest" senator, with a net worth on his 2005 Statement of Assets, Liabilities and Net worth of 3.49 million Philippine pesos. Flavier was also formerly a resident presenter on Kapwa Ko Mahal Ko, a public service programme on GMA Network.
Flavier wrote a regular newspaper column about his experiences as a doctor in the countryside, even while he served at Health Secretary. Below is a listing of works authored by Flavier, including Doctor to the Barrios, wherein he narrates his experience working with and for the Philippine Rural Reconstruction Movement.
Books
Doctor to the Barrios, Experiences with the Philippine Rural Reconstruction Movement
My Friends in the Barrios
Back to the Barrios: Balikbaryo
Parables of the Barrio: Vol. I
Parables of the Barrio: Vol. II, Nos. 51-100
Parables of the Barrio: Vol. III, Nos. 101-150
Let's DOH It!: How We Did It
From Barrio to Senado: an Autobiography
Papers
''Mobilizing Local Leaders for Rural Development: The Case of the People's School