The Supreme Court last week endorsed a decision by Duterte to allow Marcos to be laid to rest at the heroes' cemetery.
Ex-Philippine dictator Ferdinand Marcos was buried at the national heroes' cemetery in a secretive ceremony Friday, outraging opponents who said it whitewashed his brutal rule and tainted the famous 1986 "People Power" revolution that toppled him.
The burial at the "Cemetery of Heroes" was another stunning development in the remarkable political comeback of the Marcos family, a phenomenon given fresh energy this year by the clan's strong alliance with new President Rodrigo Duterte.
The Supreme Court last week endorsed a decision by Duterte to allow Marcos to be laid to rest at the heroes' cemetery, rejecting petitioners' complaints that the dictator did not deserve such an honour because of his many crimes.
The Marcos family and government then moved quickly, secretly flying the embalmed body to the cemetery on Friday and interring him despite appeals still pending with the Supreme Court urging it to reconsider.
"Like a thief in the night, the Marcos family deliberately hid the information of burying former president Marcos today from the Filipino people," said Vice President Leni Robredo, who was elected separately to Duterte and belongs to another party.
"This is nothing new to the Marcoses -- they who had hidden wealth, hidden human rights abuses, and now, a hidden burial -- with complete disregard for the law."
Marcos's 87-year-old wife Imelda -- infamous for an extravagant lifestyle during her husband's two-decade rule -- attended Friday's ceremony, along with her children and grandchildren, according to footage released by the family on Facebook.
The military honoured Marcos at the ceremony with a 21-gun salute as soldiers in parade dress and ceremonial rifles stood to attention.
Two thousand riot police and soldiers guarded the perimeter of the cemetery, blocking entry by journalists and protesters who rushed there after police confirmed minutes before that the burial was about to take place.
"I am very angry and disappointed. I am disgusted. Marcos is no hero," university student Antonio Navarro told AFP outside the cemetery.
Marcos ruled the Philippines for two decades until forced into US exile by the "People Power" revolution, a largely peaceful event that inspired democracy movements throughout Asia and around the world.
Marcos, his wife and their cronies plundered up to $10 billion from state coffers during his rule, according to government investigators and historians.
The dictator also oversaw widespread human rights abuses to maintain his control of the country and enable his plundering, with thousands of people killed and tortured, previous Philippine governments said.
Anti-corruption watchdog Transparency International in 2004 named Marcos the second most corrupt leader of all time, behind Indonesian dictator Suharto.
The Philippines' foreign debt went from $2.67 billion in 1972, when Marcos declared martial law, to $28.2 billion in 1986, according to the World Bank.
After Marcos died in Hawaii in 1989, his family was allowed to return and began its political comeback.
Imelda became a congresswoman and fended off all corruption charges against her.
Two of her children established themselves as influential politicians. Ferdinand "Bongbong" Marcos Jnr, was the more successful, becoming a senator before almost winning the vice presidency this year.
However, previous presidents had refused to allow the dictator to be buried in the heroes' cemetery because of Marcos's crimes, so the family kept the preserved body in a glass casket at his home in the northern province of Ilocos Norte.
The family's fortunes changed with the election of Duterte, a long-time ally of the Marcos family, as president in May this year.
He said Marcos deserved to be buried at the heroes' cemetery based on the fact he had been a president and a veteran of World War II.
Duterte also said he owed loyalty to the family because his father had served in the Marcos government and the family had helped fund his election campaign.
One of the Marcoses' two daughters, Imee, made a short statement after the ceremony thanking Duterte and all of the family?s supporters.
"At last our beloved father Ferdinand Edralin Marcos's final instruction to be buried alongside his fellow soldiers was carried out today," she said.
Opponents said they would hold protests on Friday afternoon.