Mr Duterte, known for his outspoken attitude, has been in trouble with bishops in the country in the past for saying he will bring back the death penalty for criminals and 'joking' about a raped and murdered Christian missionary.
The Philippines is an overwhelmingly Catholic nation, around 80% of country identify as believers.
He has alleged that the Church is full of requests for favours from politicians and has previously spoken out against the bishops, saying "don't criticise me."
The 71-year-old candidate also accused bishops of breaking their celibacy vow by marrying or asking favours, according to Asian Correspondent.
He told a story where he said church officials 'forced' him to use his role as mayor to give them land.
The former mayor of Davao City has won millions of votes already.
Speaking at a news conference he asked if the Church was ashamed of itself, saying: "Some people here in the Philippines can't even afford to have food to eat or get medicine while you're enjoying the money of the goddamn people."
He continued: "You know, the most hypocritical institution is the Catholic Church," but later apologised for his remarks.
Duterte made headlines this year by swearing about Pope Francis during his visit to the country.
The politician says he will keep discussing the "sins of the Catholic church".
He is up against the first transgender woman to run, as well as Christian boxing champion Manny Pacquiao.
