Ssemogerere made the remarks while leading Mass at Lubaga Cathedral, which was attended by Electoral Commission officials led by Justice Byabakama, as the country prepares for the upcoming Local Council One (LC1) chairperson elections.
The Archbishop questioned why the choices made by voters are sometimes altered despite citizens participating in the electoral process.
He also expressed concern over what he described as growing uncertainty and anxiety among Ugandans, saying many people are left with unanswered questions about the country's direction.
Justice Byabakama responded by urging Ugandans who believe electoral irregularities have affected election outcomes to seek justice through the courts.
He said the legal process remains the appropriate avenue for resolving election disputes and safeguarding the integrity of the electoral system.
Addressing worshippers after Mass, Byabakama called on citizens to actively participate in the forthcoming LC1 village committee elections and remain vigilant throughout the voting process.
Unlike previous elections, where voters were often encouraged to leave polling stations immediately after casting their ballots, Byabakama urged voters to remain at polling stations after voting to witness the counting of ballots and know the results firsthand.
He also cautioned incumbent village chairpersons against interfering with the ongoing voter registration exercise by registering people who are not genuine residents of their respective villages.
Uganda's recent general elections were marked by several petitions and disputes, with some candidates alleging they had won their races but were not declared victorious by the Electoral Commission. The disagreements led to confrontations at some tally centres and delayed the declaration of results in certain areas.
During the same Mass, Archbishop Ssemogerere admitted more than 30 seminarians into the ministries of Lector and Acolyte, commissioning them for service in the Catholic Church.