An airport source said Duterte arrived this morning "without fanfare" accompanied by security officials who escorted him to his vehicle.
The Herald has also confirmed that the President is ordering a Filipino banquet to be served in his room.
Duterte, 71, has had a frosty relationship with Obama and the US government since US officials expressed reservations about his anti-drug war, which is thought to have killed more than 4000 people since July.
He has told Obama to "go to hell" and announced his "separation" from America, his country's treaty ally, during a state visit to China last month.
A Filipino activist shout slogans calling for an end to extrajudicial killings related to Philippine President Rodrigo Duterte's war on drugs.
His push away from Washington has been accompanied by approaches to China and Russia.
Nicknamed 'The Punisher' and 'Duterte Harry', Duterte took office on June 30 and has promised to kill more than 100,000 drug users and fill Manila Bay with their bodies.
He has urged citizens and the police to conduct extra-judicial killings of suspects, and has said in a televised debate he would kill his own children if they took drugs.
The bodies of dealers and addicts have since been turning up in cities across the Philippines. Police statistics show a surge in the number of drug suspects shot dead by security forces, but vigilantes appear to have killed significantly more.
The United Nations, the Roman Catholic Church, the European Union and the United States have condemned Duterte's policy as a violation of human rights.
Auckland Filipino community leader and former consul general Emilie Shi said despite the controversy Duterte is "highly popular".
"He is seen as someone who dares to be different in his position and policy, and as a president who is actually doing something for the country," Shi said.
"Many here will like to meet him, but time does not permit as his trip this time is just an overnight one."
She said the alleged killings under his watch were "unsubstantiated".
Shi confirmed that staff from the embassy including the Philippines Ambassador are in Auckland to meet with this president.
Before the Apec trip, Philippine deputy Cabinet secretary Peter Tiu Lavina acknowledged the possibility of a New Zealand visit in a Facebook post outlining Duterte's recent travel movements.
"He may stop over in New Zealand to extend our vigorous efforts to build friendship among nations down to the south Pacific region," the post read.
International media have speculated that Duterte's unusual route to Apec could have been settled upon to avoid landing in the US.
