Abe is set to arrive in Manila Thursday afternoon for a two-day official visit. He is accompanied by his wife, First Lady Akie Abe.
Abe will meet Duterte in Malacañang before he flies to Davao City in the evening.
The two leaders are expected to discuss a wide range of topics, including counter terrorism, drug rehabilitation projects, infrastructure development, maritime cooperation, and development projects, the Department of Foreign Affairs said.
Abe will also talk to local business leaders and politicians in Manila and Davao.
In Davao, Abe is scheduled to visit a former Japanese settlement in Mintal, also known as Little Tokyo, which was home to Japanese migrants who established Abaca plantations in the district prior to World War II.
He is also expected to visit Duterte's home in Matina.
Abe is the first head of government to officially visit the Philippines this year.
The Philippines and Japan commemorated 60 years of diplomatic relations in 2016.
In October, Duterte said his meetings with Abe and other Japanese officials were productive in the areas of security, defense, and cooperation. He said ties between the two neighboring countries are "excellent."
Security tight for Abe visit
The Presidential Security Group is securing Abe's visit, along with the Davao City Police.
Closed-circuit television (CCTV) cameras were placed to monitor areas in and near the prime minister's itinerary, Davao's Public Safety and Security Command Center said.
The last prime minister to visit Davao City was Malaysian Prime Minister Mahathir Mohammad in 1994, authorities said.
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Davao City-based journalist Ben Tesiorna contributed to this report.