Egan was later appointed Secretary of the Archdiocesan Commissions on Ecumenism and Human Relations, sitting on several interfaith organizations and establishing dialogue with Jews and Protestants alike. From 1969 to 1971, he served as co-chancellor for the archdiocese. Egan once again returned to Rome in 1971, when Pope Paul VI named him an auditor of the Sacred Roman Rota. While serving on the Roman Rota, he was also a professor of canon law at the Gregorian and of civil and criminal procedure at the "Studio Rotale". Egan served as a commissioner of the Congregation for the Sacraments and Divine Worship and a consultor of the Congregation for the Clergy as well. In 1982, he was chosen to be one of the six canonists who reviewed the new Code of Canon Law with Pope John Paul II before its promulgation in 1983.