Arrested were businessman Norberto Antiquando, 37; alleged hired gun Alan Inot, 39; Claudio Bontilao, 39, and Alex Oyao.
Director Nestorio Gualberto, chief of the Criminal Investigation and Detection Group (CIDG), said Antiquando masterminded the killing of Masayuki Kuwabara after the Japanese allegedly swindled him in the export of handicrafts.
"Antiquando often paid the customs duties and fees for shipping the handicrafts to Japan," he said. "And (Kuwabara) would often yell at him."
Gualberto said Antiquando was the first to fall in the hands of detectives following up the case.
Investigators said Kuwabaras actions angered Antiquando that he sought Bontilao and Oyao to look for a hired gun who would kill Kuwabara.
The two were able to contact Inot, who took the job, they said.
Investigators said the motorcycle-riding Inot tailed the chauffeur-driven car of Kuwabara and compatriot Yushiyaki Mewa, and fired at them at the intersection on Bantilad Road near Gaisano Supermall.
Kuwabara died on the spot after being hit in the head, while Mewa, who was wounded in the face, is fighting for his life at an undisclosed hospital.
Kuwabara was a frequent visitor to Cebu, where he bought fiberglass for his company in Japan, while Mewa, who lives in the city, acted as his technical consultant.
Mewas driver, who survived the attack, told investigators the killer took a brown envelope from Kuwabara before fleeing.