The ceremony began with a 21-gun salute as soldiers in parade dress and ceremonial rifles stood to attention at the "Cemetery of Heroes" in Manila, after his body was secretly flown to the venue in an apparent effort to avoid protests.
The Supreme Court said last week that Marcos, who ruled the nation for two decades until millions of people took to the streets in the 1986 military-backed uprising, could be buried at the heroes' cemetery.
The surprise move by the Marcos family and the government to bury him so quickly after the Supreme Court verdict, with appeals still to be heard, caused further outrage.
Barry Gutierrez, counsel for the anti-Marcos court petitioners, said the burial was illegal because of the outstanding appeals.
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"It's not really surprising that this is happening. Marcos flouted the law when he was still alive, and even at his burial, he is still breaking the law," Gutierrez told AFP.
"We are shocked and angered," Gutierrez said.
Thousands of riot police and soldiers guarded the perimeter of the cemetery, but there were no protesters.
Journalists who rushed to the cemetery were barred from entering. However reporters were able to view the ceremony with long camera lenses from outside.
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.
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.