Duterte's strong remarks are believed to have been made in response to the Catholic church's opposition to his government's ongoing war on drugs, which has left thousands dead.
According to local reports, Duterte's comments were made during a speech at the presidential palace on Wednesday.
According to local media reported that President Duterte accused the Catholic clergy of doing nothing else but criticise, Al Jazeera said.
'These bishops that you guys have, kill them. They are useless fools. All they do is criticise.'
Duterte was reportedly giving a speech to local government officials when he began his diatribe against the Catholic Church again, calling it "the most hypocritical institution" and saying his God is different from the one Catholics worship.
More intriguing is the fact that Duterte himself is, on paper, a Catholic.
It is not the first time that President Duterte has attacked the Catholic church which has alarmed the church's faithful, who make up about 90 percent of the country.
The Catholic church has also made their concerns known, following the death of three of its priests since December 2017.
However, Duterte has hit back at the church on various occasions about church morality in light of the high-profile international sexual abuse scandals involving priests.
It is not the only thing the Filipino president has said which has shocked public opinion with his off-the-cuff remarks - even having to apologise for calling former US President Barack Obama 'a son of a w***e' back in 2016.
Earlier in the week, he said he had used marijuana to stay awake, but quickly backtracked on his remarks, stating that he was just joking.
However, not everyone found the president's joke very funny, and a local senator challenged Duterte on Thursday to take a drug test to prove it.
Rough police estimates suggest that nearly 5,000 suspected drug dealers and users have been killed since Duterte announced his war on drugs, while rights groups say the true toll is at least triple that and may amount to crimes against humanity.
In November, three Philippine policemen were sentenced to up to 40 years in prison without parole, for murdering Kian Delos Santos, during an anti-narcotics sweep.
President Duterte has vowed to pardon authorities involved in the deadly bloody crackdown, but even he refused to defend the 2017 killing in a dank Manila alley.
Duterte's spokesman Salvador Panelo also welcomed the ruling as he gave assurances the president opposed 'intentional killing'.
He added: 'It shows that this country has a robust judicial system.'
Police said the teenager was a drug courier who fired at them while resisting arrest.
However, CCTV footage and witness accounts revealed two of the policemen dragging the unarmed boy moments before he was shot dead.
Drug war critics hailed the conviction as an example of justice and accountability, which they said have been rare since Duterte unleashed the campaign to rid the Philippines of narcotics in 2016.
Duterte and his drug war are backed by many Filipinos fed up with high crime rates and a slow-moving judicial system.
But the death of Santos, as well as of two other Manila teenagers accused of robbing a taxi driver, triggered rare street protests in 2017 and highlighted concerns about police abuse.
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