In 1960 he was appointed Secretary General of the Catholic Bishops Conference of India, and later served on two Vatican Council commissions under Pope John XXIII.

Fernandes lectured on religion and philosophy and on educational and cultural matters to all types of audiences in India, the Far East, Australia, New Zealand, Ireland, Great Britain, Belgium, Netherlands, Switzerland, Germany, Denmark, Italy and all parts of the United States.

He undertook a World Tour under the auspices of the Christian Family Movement in connection with Ecumenical Meetings on Development, Justice and Peace.

In connection with multi-religious work in the fields of human rights, development, disarmament, environment he travelled to Turkey, Scotland, England, Finland, the United States, Japan, Singapore, Bangladesh, Malaysia, Hong Kong, Thailand, Philippines, Indonesia, Pakistan, various European countries and Canada.

He also visited Sri Lanka, Burma, Iran, Aden, Mauritius, Israel, Portugal, Spain, France, Poland, Sweden, East Germany.