The practice was suspended in Newry, Co Down, as a precaution following virus cases in Britain and the Republic of Ireland.
The move came after an alarmed parishioner wrote to Dominican Chapel prior Fr Gerard Fearon calling for action.
Fr Fearon said: "It was in response to an anonymous letter from a parishioner who disagreed with the Sign of Peace.
"I just thought we would suspend it for a while in the context that scientists are saying that we should be protecting ourselves against swine flu and how it is important to have clean hands."
He told the Newry Democrat the Sign of Peace would be suspended at Dominican services this weekend.
"I told parishioners that it would be back again once the health authorities have given absolute clearance.
"It was just something to laugh at more than anything. I wouldn't take it too seriously."
One parishioner said he was surprised at the length the church was going to.
"It does seem a bit over the top," he added.
There have been no confirmed cases of swine flu in Northern Ireland.
A spokeswoman for the Catholic church in the Republic said they have had a number of inquiries but were telling people to follow the Health Service Executive (the Republic's health authority) advice.
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