The Pastoral Commission is primarily concerned with propagating and consolidating the faith in the Diocese. It operates under the following committees: Executive, Liturgical, Catechists, Biblical and Catechetical, Social Communication, Vocation and Missionary Animation.

Liturgical Committee: It organizes courses for choirmasters as well as Parish choirs. It sets up inter parish choir competitions. The committee has a task to translate several liturgical materials into the local language.

Biblical and Catechetical Committee: This committee helps to form Bible groups in the Parishes for the purpose of spiritual renewal through Bible study and sharing. It encourages each individual to have a Bible and gives some tips on how best to use it. The Bible is the basis of Christian instruction and each child that comes for catechumenal course has to have one. This committee has also to study and identify the positive elements in our cultural traditions so as to integrate them with our Christian faith. At the same time, it has to fight vigorously against negative traditional elements that obscure the understanding and living of the Gospel.

The Catechists Committee: The Catechists work very closely with the Priests and the Religious in the pastoral ministry. This committee has a director who is a Priest and is in charge of the formation of catechists at Villa Maria catechists training center. The director works hand in hand with the catechists executive that is headed by the head of the catechists in the Diocese (Ssabasomesa). The catechists committee is guided by the catechists constitution. It organizes on-going formation courses for catechists and their spouses, campaigns for vocations to the catechetical ministry, as well as Priesthood and Religious life. It organizes retreats for catechists and sets up socio-economic projects for the welfare of the catechists. The catechists are instrumental in making a follow up of the established small Christian communities and the entire pastoral ministry in their respective areas of operation. However, many catechists are very old in age. There is great need to urge the young generation to become catechists and to have them trained at the catechetical center.

Ecumenism and interfaith dialogue committee: This committee guides the Catholics in the Diocese on how to relate with other churches and denominations in the Diocese. It has published a booklet to give Catholics guidelines in matters related to ecumenism and interfaith dialogue. There is a cordial relationship between the Catholics and Protestants in the Diocese. There are some activities, which are jointly celebrated together in the spirit of ecumenism. These are: the unity week, and the liturgical celebration of the Way of the Cross-on Good Friday.

Vocations and Missionary animation committee: It has a task to promote vocations in the Diocese and to cultivate a missionary spirit in the local church through the office of PMS (pontifical missionary society). A team headed by the vocations director has to go round the Diocese promoting vocations among children and the youth in schools and other institutions. Generally Masaka Diocese is still blessed with vocations to Priesthood and Religious life. There is an urgent need to obtain more benefactors both here and beyond the Diocese to assist candidates especially from poor families. The Christians are urged to participate in the training of seminarians through paying cost sharing.

The task of missionary animation is fulfilled through the Diocesan PMS office. This committee organizes the celebration of the scheduled PMS days. On those days, prayer for the missions, the solidarity of the local church with the universal church, are emphasized. Special collections are made in the churches throughout the Diocese and sent to the National PMS offices. Through the PMS office, assistance is received from Rome towards the construction and renovation of churches, Priests presbyteries, convents, schools and hospitals.

The Communication committee: The committee is responsible to promote Evangelization through communication. It publishes the Diocesan periodical, AGAFAAYO, in which among other things the activities and progress of the evangelization mission in the Diocese is given. It has a task to make use of the local FM radios and to ensure that each Parish has a public address system to enable the churchgoers to hear the word of God and to participate actively in the liturgical celebrations.

The Deans committee: The Diocese has eleven established Deaneries, each of which is headed by a Dean. The Deaneries serve the purpose of decentralization in view of bringing the church services nearer to the people. The Deans periodically meet to evaluate and plan the pastoral activities in the Deaneries. 

The Association of the Religious in Uganda (ARU) Masaka branch, Committee: This committee brings together the different Religious congregations that work in the Diocese. Through this committee, the spirit of unity and cooperation is promoted among the Religious. They have some pastoral activities in the Diocese they have organized to carry out together; for instance the pastoral work in the prisons.