About 2,000 people gathered in heavy rain to denounce Duterte's plans to move Marcos' remains from his northern hometown to the National Heroes' Cemetery in the capital, Manila, next month.
"We would be the laughing stock of the entire planet," Senator Risa Hontiveros, one of four members of parliament to attend the Manila rally, told AFP.
She called Marcos an "unrepentant enemy of our heroes".
Marcos's family have kept his preserved body on display after he died in exile in 1989 following a popular revolt three years earlier, demanding that it be buried with full honours in the Heroes' Cemetery.
But Duterte, who has styled himself as an anti-corruption crusader, defended Marcos, noting that his father had served in the Marcos cabinet and he himself had even voted for Marcos before.
Duterte has previously said that he won the May 9 elections partly with the support of the Marcos family who remain influential in their bailiwick in the northern Philippines.
A small protest was also staged by human rights victims outside Duterte's southern hometown of Davao city, where candles and flowers were placed outside the city hall, television reports said.
Protesters shed tears during the three-hour protest and organisers launched a signature campaign to try to reverse Duterte's decision.
"I was jailed when I was young. It's so hard to imagine that he will be buried in the Heroes' Cemetery," former Marcos prisoner Danny Tang told AFP.
University of the Philippines Professor Ricardo Jose alleged that in order to win war medals for bravery, Marcos faked his service record in the anti-Japanese resistance when Japan occupied the country in World War II.
Duterte spokesman Martin Andanar told reporters today that while the leader allowed protests against the burial plan, he "remains firm" it will be carried out.
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