The Diocese of Down and Connor has also told priests to disinfect their hands before distributing Holy Communion, while offering wine from a shared chalice has been temporality stopped.
The measures have been taken as a strain of influenza known as Australian flu is contributing to pressures on the NHS this winter.
Fr Edward McGee told Premier why Catholics shouldn't oppose the measures.
Speaking during Premier's News Hour, he said: "Our faith tells us - yes we act in faith but also that God gifted us with the gift of reason.
"So we also must respond [to] the advice and guidance of those that are experts in this area.
"The healthcare professionals are the instrument of God's care in the world as well.
"So to follow their advice is actually to cooperate with the grace of God in trying to respond in the most reasonable and rational and caring way to those who are vulnerable in our society at this time."
The priest said the church was told by a public health agency to do more to prevent the very infectious strain of Influenza.
He explained: "They indicated that we move beyond pre-epidemic thresholds.
"The indications now are that the Australian flu has quite a severe impact on people."
The diocese last implemented infection prevention measures during the swine flu epidemic in 2009.
Listen to Fr Edward McGee speaking with Premier's Eno Adeogun: