During the visit, he officially announced the completion of a 732-meter Youtefa Bridge in on Monday. It connects the provincial capital Jayapura and Muara Tami district.
He also visited several districts in the two easternmost provinces with crowds gathered waiting at the town square to welcome him with a traditional dance performance in the morning.
He arrived by helicopter at Arfak Mountain district in the morning accompanied by first lady Iriana, Indonesian Military (TNI) commander Air Chief Marshal Hadi Tjahjanto, Home Affairs Minister Tito Karnavian and Public Works and Housing Minister Basuki Hadimuljanto.
He said he visited the area at the request of the district head and the governor, to take a firsthand look at the district.
The Indonesian news agency Antara reported that residents started to gather at the square at 5.30 am to wait for his arrival.
Indonesia deployed 1,000 security personnel to Papua after violent protests that saw buildings torched and street battles between police and demonstrators.
Hundreds marched through the streets of Sorong city, and in the town of Fakfak on the western edge of the island, which is divided between Indonesia and the independent nation of Papua New Guinea.
Several cities in the resource-rich Papua were brought to a standstill. In Manokwari, angry demonstrators set ablaze businesses and the local parliament building.
Jokowi said he listened to all proposals by the district head, and infrastructure development.
He said road infrastructure development must commence immediately, so agricultural products from here can be distributed to Manokwari or other provinces.
Jokowi posted on Twitter saying thousands of people had showed up for the gathering.
He took a selfie with residents during his visit to Kaimana district in West Papua on Sunday.
He also visited Manokwari — the provincial capital — and Kaimana district, before ending his trip in Papua’s Jayawijaya district.
At least 30 people were killed in riots in several districts, most notably Wamena and Jayapura, while many Papuan students left their campuses in Java in protest of unverified abuse, says The Jakarta Globe.