The incident involving the man occurred in Cill Mhuire Church in Ballymany, outside Newbridge, and was unconnected to the burglary.
It came to light when the church’s curate, Fr Ruairi O'Domhnaill, was reviewing CCTV footage after a burglary at the church.
The recording clearly showed a man, whose identity is as yet unknown, coming into the church, undressing, and sitting on the altar for approximately two minutes.
The poor quality of the CCTV footage has left investigators unsure as to whether the man kept his underwear on.
He then put his clothes back on and walked out of the church.
The priest was reviewing the footage to see who tried to steal a donation box and shrine collection.
Gardaí at Newbridge are now investigating both incidents at the church but still have not identified the people involved.
Sergeant Seamus Rothwell confirmed the matter was under investigation and added that “at this stage, we don’t get surprised no matter what we see.”