More than 1,000 mourners gathered at the St. Sebastian church in the coastal city of Negombo, just north of the capital, Colombo, where more than 100 parishioners were killed as they worshipped on Sunday morning.
The ceremony began with prayers and singing under a tent put up in the church courtyard. Pall-bearers dressed in white then carried in the coffins one by one.
Relatives gathered around the wooden coffins, crying and comforting each other. Some were overcome by the grief and sweltering heat and needed support from family members.
Cardinal Malcolm Ranjith, the archbishop of Sri Lanka who led the service, urged other churches to delay memorials amid fears that more bombers may be at large.
"The security forces have not cleared the situation yet ... there could be more attacks on public gatherings," he told reporters.
"I urge priests to not conduct any services at churches until I notify."
No group has claimed responsibility for the attacks on three churches and three luxury hotels that came within 20 minutes during Easter services and as hotels served breakfast.
Most of the 321 dead and 500 wounded were Sri Lankans, although government officials said 38 foreigners were killed.
The bombs shattered a relative calm in the Buddhist-majority Indian Ocean island since a bitter civil war fought by Tamil separatists ended 10 years ago and raised fears of a return to sectarian violence.
Sri Lanka's 22 million people include minority Christians, Muslims and Hindus.
Up to now, Christians had largely managed to keep out of the worst of the island's conflict and communal tensions.
A senior Buddhist leader who attended the St. Sebastian service appealed for unity.
"Buddhism is about love and compassion, so is Catholicism. The roots are the same. I have come in this spirit," said Chief Incumbent of the Dharmayathanaya Temple, Venerable Elle Gunawansa Thero."In this country we are branches of the same river, of the same tree. We have to stick together," he said.