From 1953 to 1954, Whitaker was the chairman of the Catholic University Youth of Brazil, formed by Catholic University students from all over the country. He then served on the strategy group of São Paulo governor , which spanned from 1959 to 1963. He was also head of land reform planning during the João Goulart administration. Following the coup d'état that overthrew Goulart, he joined the opposition movement against the military dictatorship. From 1965 to 1966, he was an advisor of the National Conferences of Bishops of Brazil ("Conferência Nacional dos Bispos do Brasil, CNBB") at the First Joint Pastoral Plan. In 1966, fleeing political persecution in the country, he went into live in exile with his wife and four children.