In 1963, he founded the Ecumenical Christian Centre in Bangalore and developed it into a meeting place of people of all religious and political views. The Rev. Dr. Thomas served as the President of the India Section of Amnesty International and Association of Christian Institutes for Social Concern in Asia.
It was the Emergency rule of 1975 that galvanized the Rev. Dr. M.A. Thomas into action. The denial of democratic rights by the administration and the failure of the people to react strongly against it caused him great anguish. After much deliberation, he launched the new national level human rights organization Vigil India Movement in 1975.
Vigil India Movement was officially inaugurated in 1977 after the lifting of the emergency rule. He passed away on June 25, 1993. The Board of Trustees of Vigil India Movement instituted the M.A. Thomas National Human Rights Award in 1993 to honour the memory of this practical ecumenist and humanist.