The Evangelical Protestant Society (EPS) had written to the Dean of St Patrick's, the Very Rev Dr Robert MacCarthy, demanding an end to the sale of rosary beads in the cathedral shop.
Secretary of the organisation Wallace Thompson said he had been on a visit to the cathedral recently when he noticed the items.
"I was really quite surprised," he said.
"I came home and thought I should write to the Dean to say we were concerned and ask him what his reaction was. He came back very quickly to me and his reaction was very clear."
Mr Thompson, who is also a DUP special advisor to the Northern Ireland Executive, said he was "not at all" satisfied with the Dean's answer, which stated that the beads were sold because most of the visitors to St Patrick's were not Anglican.
"My argument is that it's a silly principle because if you pander to what people want it might not be what people need," Mr Thompson said.
"In a Protestant church I don't think they should be selling things that are Roman Catholic.
"I think you need to give people what you believe is in their best interest. A Protestant church should stock Protestant literature, not things like that."
Speaking last night, Dr MacCarthy pointed out that rosary beads had been sold in the shop since 1970 and would continue to be sold there.
"We have done so for 37 years," he said.
"They are obviously much in demand because we get €70,000 gross a year from the sale of rosary beads.
"As far as I'm concerned the majority of visitors to the cathedral are not Anglicans, never mind Evangelical.
"We get about 320,000 visitors a year. If a large number of those want to use rosaries as visual aids in their prayers we're delighted.
"I get about two letters a year objecting to the sale of rosary beads usually from Northern Ireland addresses."
The EPS, which was founded in 1946, is described on its website as an " inter-denominational Protestant voice in the 21st Century" and counts around 3,000 supporters, most of whom are based in Northern Ireland.
Its aims are "to promote and defend the tenets of historic Biblical Protestantism and to fulfil the role of an umbrella organisation uniting Protestants of different churches and backgrounds".
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