A controlled explosion was carried out by Army bomb experts on a suspicious object found in the church grounds on Saturday evening.
The security alert was later found to be a hoax, but it still meant Mass had to be moved to another church at the last minute.
Father Anthony Alexander told UTV: "It's sad - it's very, very sad that people do that sort of thing. I don't know what they're trying to prove."
The alert began when police arrived just as the church was being opened up to prepare for the evening's service.
One great thing was the great support - local Presbyterians rang me last night and offered their support and they were praying for us this morning.
Father Anthony Alexander
"It upset the old people and I feel sorry for the people who live across the way," Father Alexander said, but he insisted they would only treat the incident as "an inconvenience".
He added: "I don't know what the point is, but I'm not going to let it affect us or affect the parishioners. We will still worship God and that's all we can do."
Roads in the area were closed for a number of hours before the alert was lifted.
The latest alert comes after two pipe bombs were left at the door of a Catholic church in Ballyclare on Friday. School children had to be escorted from Sacred Heart Church during the alert.
Police said on Sunday that no definite leads had emerged as to who left the bombs there.