Philippine officials said Isnilon Hapilon, Daesh's "emir" in Southeast Asia and Omarkhayam Maute, one of two Middle East-educated "Khalifas" at the helm of the militant alliance, have been killed.
Although opposition legislators questioned government officials for hours on the legality of the move, the vote was largely a foregone conclusion as Duterte enjoys majorities in both houses of Congress.
The Filipino government placed Mindanao, an island of 22 million people, under martial law on May 23 "to crush" militant groups linked to Daesh.
The Philippines has a long history of conflict. Over the past few decades, homegrown militants, particularly in the south of the country, have stepped up their campaigns against the government.
As the battle for Marawi City on Mindanao island enters its fifth week, pro-Daesh militants stormed a school in the south of the island and briefly held people there captive. There were no reports of casualties.
Around 10,000 orphans seek refuge in a Turkish-run orphanage on the troubled southern Philippine island of Mindanao.
The Philippines military confirms the US is providing technical assistance, but it had no boots on the ground. Thirteen Philippine marines conducting clearing operations have been killed in the battle for Marawi city, a military spokesman said.
The authorities in the Philippines have hit the rebels' logistics hard, cutting off key supplies and seizing large amounts of weapons and explosives.
The military says that rebel fighters are penned into a built-up area of the city. Troops have been clearing houses that the militants used as sniper positions for the past two weeks.
The Phillipines' president has offered $410,000 for the "neutralisation" of Isnilon Hapilon, Abdullah Maute and his brother Omarkhayam Maute. The three are said to be the leaders of the militants fighting troops in Marawi.
The violence that began last week has killed dozens. Though most people have left, those still trapped are worried about being intercepted by militants at checkpoints on routes out of the city.
Daesh-linked Maute militants targeted the civilians in the mainly-Muslim city of Marawi on Mindanao island raising the death toll to 85 since the fighting began five days ago, military officials say.
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