The apology is likely to soothe frustrations among religious minorities who feel that overzealous government authorities and clerics are trying too hard to champion the interests of Islam and ignoring the rights of non-Muslims.
The Al Islam monthly magazine, which focuses on issues affecting Malaysian Muslims, acknowledged in a statement on its publisher's Web site that its article had "unintentionally hurt the feelings of Christians, especially Catholics."
Al Islam's article, published in May last year, was meant to investigate rumors that Muslim teenagers were being converted to Christianity in churches. The article said its two reporters had found no evidence of that.
The apology came after Archbishop Murphy Pakiam, who heads the Catholic Church in peninsular Malaysia, criticized government authorities earlier this week for not prosecuting the two men who researched the article. Pakiam, however, said that church leaders would be satisfied if the magazine issued a formal apology.
Attorney General Abdul Gani Patail responded that no charges were filed because the two men committed only "an act of sheer ignorance" without any malicious intention.
The magazine's statement Saturday said it "never meant to insult the Christian faith, let alone to disturb or trespass into its house of worship."
"The Al Islam magazine apologizes in connection with the publication of the article," the statement said, adding that its two writers were also sorry and had been unaware that their actions would offend Christians.
The men had spat out Communion wafers and took a photograph of a partially bitten one. Catholics believe the Communion wafer is transformed into the body of Christ by the priest during Mass.
Non-baptized persons are not allowed to receive Communion in the Catholic church. While the church allows non-Catholics to attend Mass, many Catholics in this case were unhappy the two men entered the church under false pretenses.
