The recording artist, famous for songs including 'Vogue', 'Pappa Don't Preach' and 'Like a Virgin', has been criticised by Christians in the past for using religious symbolism and clothing in songs.
Archbishop William Goh has said that many voices in the Church are upset by the singer's "disrespectful use of Catholic and Christian symbols".
He has warned believers not to support anyone who is seen to "denigrate and insult religions".
Who is Madonna?
Name: Madonna Louise Ciccone
From: Bay City, Michigan, U.S.
Net worth: U.S. $520 million
Tours: 10 world tours
He even met with government officials to express his worry about a concert in Singapore on Sunday, which is part of the American singer's Rebel Heart tour.
It will be Madonna's first performance in Singapore, a largely conservative nation, since she was banned from performing in 1993 after police said her performances are "objectionable to many on moral and religious grounds".
In a statement posted on the diocese website, the archbishop said: "It is our moral obligation not to support those who denigrate and insult religions, including anti-Christian and immoral values promoted by the secular world.
"There is no neutrality in faith; one is either for or against. Being present (at these events) in itself is a counter witness."
"Obedience to God and His commandments must come before the arts. As the people of God, we should subscribe to authentic Arts that lead us to God through the appreciation of beauty, harmony, goodness, truth and love, respect, unity and the transcendent; and not support the 'pseudo arts' that promote sensuality, rebellion, disrespect, pornography, contamination of the mind of the young, abusive freedom, individualism at the expense of the common good, vulgarity, lies and half-truths."
The Media Development Authority in Singapore has restricted who can attend the concert, which will be held in the 55,000 seat National Stadium, to over-18's due to references to sex.
Local media has been reporting that Madonna will not perform the 'Holy Water' part of her tour, where dancers dressed as nuns perform on poles shaped as crosses.