The Marcos family had put the patriarch's corpse on public display at his ancestral home in the northern Philippines
Some 3,000 protesters marched on a central Manila park to demand that President Rodrigo Duterte and the Supreme Court remove the body from the cemetery, a week after the long-dead former president's interment.
Marcos died in exile in Hawaii in 1989, three years after a bloodless "People Power" revolution ended a 20-year rule historians say was marked by massive corruption and the imprisonment, torture and murder of thousands of critics.
"His burial there violates not only the rights of the victims but also the entire idea of justice itself," Ephraim Cortez said as he and a dozen fellow lawyers joined the protest, wearing Marcos masks daubed with red swastikas.
Many of the protesters were students who walked out of their classrooms at universities around Manila and took to the streets despite rains brought on by Tropical Storm Tokage that was scything through the centre of the country.
Some carried mock coffins, including one that portrayed Marcos as Dracula.
In one novel protest action, at least 20 masked male members of a school fraternity removed their clothes and streaked past classrooms at Manila's state-run University of the Philippines.
About a thousand spectators cheered and raised posters that read "Marcos No Hero", "Never Forget" and "Remove Marcos from the LNMB", the Filipino acronym for the cemetery.
The Marcos family had put the patriarch's corpse on public display at his ancestral home in the northern Philippines for more than a decade, demanding that the government fulfil his dying wish to be interred at the heroes' cemetery.
The election this year of Duterte, the family's political ally, finally made that possible, with the Supreme Court upholding his decision on grounds Marcos deserved to be buried there as a former president and ex-soldier.
Duterte said Friday he disagreed with the protesters but upheld their right to free expression, ordering police to allow protest actions even without government permits.