Within the National Catholic Welfare Conference, he served two terms as vice- chairman (1950–52, 1956–58), two terms as chairman (1952–55, 1958–62), and one term as secretary (1962–66). As chairman of the NCWC, he issued a protest against religious and racial discrimination in June 1960. Between 1962 and 1965, Alter attended all four sessions of the Second Vatican Council, having previously served on the Central Preparatory Commission. At the Council, he sat on the Commissions for Bishops and for the Government of Dioceses. He discontinued first grades in Cincinnati parochial schools in 1964 because of high costs and overcrowded classrooms. However, Alter did not believe that this would greatly interfere with children's religious education.