The 71-year-old overthrew the political establishment at the polls, promising a “bloody war” on crime and corruption.
In his inaugural speech the controversial former mayor of Davao City promised to make sweeping changes to the country’s political system.
However, in a nod to his critics Rodrigo Duterte also insisted that he “knows the limits” of his power.
Rodrigo Duterte, who has barely left Davao in the south since his election win, took his oath at a small ceremony at the Malacanang Palace in Manila.
Only state media were permitted to cover the event, but it was streamed live online.
Rodrigo Duterte told the audience he would tackle an “erosion of the people’s trust” in the leaders, the judiciary and public servants.
He added: “As a lawyer and a former prosecutor, I know the limits of the power and authority of the president. I know what is legal and what is not.”
“I know that there are those who do not approve of my methods of fighting criminality. They say that my methods are unorthodox and verge on the illegal.
“My adherence to due process and the rule of law is uncompromising. You mind your work and I will mind mine.”
Rodrigo Duterte also promised to honor international treaties and respect peace deals agreed with rebels at home.
The new vice-president, Leni Robredo, was sworn in at a separate ceremony in Quezon City, in the suburbs of Manila.
Both will both serve a single six-year term.
The two swearing-in ceremonies were being held separately for the first time in the Philippines, which local media attributed to Rodrigo Duterte’s decision to a opt for a relatively small event.
However, there is a notable political and personality gulf between the two leaders.
Leni Robredo, an anti-poverty campaigner and human rights lawyer, was sworn in by the chairman of the poorest ward of a district in her province, as well as the chairman of the ward in which her new office is located.
She won her new position by a wafer-thin margin against Ferdinand “Bongbong” Marcos, the son of late former dictator Ferdinand Marcos, whose family has staged a remarkable political comeback since being toppled in 1986.
Leni Robredo is from the same Liberal Party as outgoing President Benigno Aquino III, who oversaw big improvements in economic growth and foreign investment.
Benigno Aquino had less success tackling endemic corruption and inequality, something Rodrigo Duterte has promised to change.
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