The prayers were held amidst tight security and frisking of the participants.
The churches had cancelled prayers for two consecutive Sundays after the attacks following security alerts.
Catholic schools are still closed and are likely to open on Tuesday depending on security conditions.
Nine suicide bombers were involved in the Easter day attacks targeting hotels and churches across the country.
Archbishop Cardinal Malcolm Ranjith has that all politicians and the leadership of the country who neglected their responsibilities should be removed from power.
Meanwhile, security crackdown on suspects continue and country’s army chief said over 85 percent of suspects linked to fundamentalist groups have been taken into custody.