They said 39-year old Imamura Kiyoto was arrested on Thursday in connection with the robbery of a store in Kyoto City on May 2, 2022.
At the time of the crime, Imamura was detained at an immigration facility in the Philippines, where he is believed to have given the robbery orders over his mobile phone.
He is suspected of recruiting the perpetrators of the Kyoto theft by offering them a "dark" part-time job, and having them procure weapons and rental cars and inspect the shop before robbing it.
Imamura was deported from the Philippines in February with several other men believed to be senior members of the group. He was arrested in Japan on suspicion of a separate fraud case.
Japanese police have arrested other people suspected of being linked to a series of thefts across the country in recent years, some of which involved assaults leading to at least one death.
Luxury watches stolen in Kyoto
Thirteen people have previously been arrested in connection with the theft of 41 luxury watches from the Kyoto shop, worth about 70 million yen. The police identified Imamura as the person who coordinated the crime, based on analysis of confiscated mobile phones and bank records showing cash transferred to Imamura's account.
The Tokyo Metropolitan Police plan to set up a joint force with prefectural police in Kyoto, Hiroshima, Yamaguchi and Chiba to investigate possible links with robbery cases across the country.
Imamura is the first alleged senior member to be arrested in connection with the robberies.
Police believe Tokyo robbery-murder case connected to group
Another case Metropolitan Police believe to be connected to the group took place at a house in Komae City, Tokyo. On the evening of January 19, a 90-year-old resident was found dead with her face bloodied and her hands tied.
Tokyo police made the discovery after they went to the scene on a tip from the Chiba Prefectural Police that the house may be targeted by robbers.
Chiba police discovered the information while investigating a robbery and injury case at a thrift store in Oamishirasato City that occurred few days before.
Investigators found the Komae City victim's home address in the mobile phone data of a person linked to their search.
Three men allegedly broke into a thrift shop on January 12. Police said the suspects beat and injured the shop's owner but left without taking anything.
They were arrested and charged with robbery and trespassing.
One of them was a 23-year old former Ground Self Defense Force officer from a unit in Mie Prefecture who had been missing since November 25, 2022. Police said he drove two accomplices in a rental car to the scene.
Suspects allegedly organized crimes from Philippines
Imamura and three others are suspected of orchestrating the series of crimes across Japan from inside a detention center in the Philippines, with which Japan does not have an extradition treaty. Police said the group may have netted more than 6 billion yen, or about 44 million dollars.
They allegedly recruited people in Japan through social media and provided instructions through chat apps, using aliases like "Luffy" or "Kim."
The four were held at the Philippine immigration bureau's Bicutan detention center for people found to be staying in the country illegally. According to others held there in the past, some detainees were permitted to use their mobile phones and laptops in the facility by bribing staff members.