Duterte, 71, was leading by more than 6 million votes over his closest rival, with votes from 90.79 per cent of precincts tallied by the Parish Pastoral Council on Responsible Voting (PPCRV).
The mayor of the southern city of Davao had 15.05 million votes so far, followed by administration candidate Mar Roxas, who received 9.01 million votes.
Third-place finisher Senator Grace Poe, who received 8.42 million votes, conceded defeat late Monday to Duterte.
Duterte, nicknamed "the Punisher" for his tough talk against crime, shocked the country during the campaign as he often cursed in his speeches and even joked about rape.
He once said that Manila Bay would turn red from the bodies he will dump there and that "God will weep" if he becomes president.
On Monday, he toned down his language and called for healing after an acrimonious campaign for the welfare of the country.
"I offer my hand in friendship to those who were my opponents in this elections," he said. "It's time for healing."
In the vice presidential race, Congresswoman Leni Robredo overtook the only son and namesake of late dictator Ferdinand Marcos in a tight contest.
Robredo was leading with 80,900 more votes than Marcos, popularly known by his nickname "Bongbong."
The PPCRV has been accredited by the Commission on Elections to conduct a quick count based on actual election returns. The official tally will later be conducted by Congress as required by law.
The commission said voter turnout in Monday's polls was estimated at 80 per cent. More than half of the predominantly Catholic country's 100 million people - or 54 million - were registered to vote.
- DPA