The ABS-CBN network withdrew t-shirts saying "No Race. No Religion. I embrace diversity."
It was marketed with the Twitter hashtag PopeTYSM, the latter half meaning "Thank you for the compassion" in the Filipino language Tagalog.
The message was meant to refer to perceptions that Pope Francis is open, progressively-minded and reformative.
But Archbishop Socrates Villegas, the president of the Catholic Archbishop's Conference of the Philippines, said the t-shirt's message was "misleading and quite frankly erroneous."
"We urge our Catholic faithful not to patronise items with misleading posts and statements.
"Francis has never said and taught that religion and race do not matter, because they most certainly do.
"It is what selfish, uncharitable and judgmental people do with religion and race that is a problem."
Three other t-shirts celebrating Pope Francis' visit remain on the market. They each say: "Who am I to judge?", "Thank you for the compassion" and "Speak less, act more."
The Holy Father begins his four-day visit in Manila, the capital of the Philippines, on January 15th.
He will meet the Philippines president Benigno Aquino, and survivors of super-typhoon Haiyan.