Cardinal Malcom Ranjith, the archbishop of Colombo, offered a televised Mass from his residence that was attended mostly by priests and nuns.
A letter from Pope Francis addressed to him was read out at the end of the service in which the pontiff said he prayed that "hearts hardened by hatred may yield to His will for peace and reconciliation among all his children".
At St Anthony's Shrine in Colombo, one of the sites targeted by Easter suicide bombings that killed 257 people, a Mass was celebrated for a small group of children and youth as a means for inner healing.
Almost all churches remained closed with armed soldiers and police guarding them.
Authorities cancelled Sunday services after reports emerged that a Catholic church and lay institution could be targeted this weekend.
Catholic schools have also been closed until further notice.
However, all government schools are to reopen Monday for grade six and up.
Police have announced they will search the premises of all schools on Sunday.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.
