The raid covered five offices of yakuza groups, including the headquarters of Yamaguchi-gumi in the western city of Kobe and the head office of Kodo-kai, a core group of Yamaguchi-gumi, in the central city of Nagoya and an office of Sumiyoshi-kai in Tokyo.
The searches were conducted by investigators from five prefectural police departments, including those of Chiba and Fukuoka.
In the May 2016 fraud, the money was illegally withdrawn simultaneously at convenience store ATMs in 17 prefectures, including Tokyo, Aichi and Osaka, with forged cash cards using customer information from South Africa's Standard Bank.
The stolen cash may have been passed on to yakuza groups, investigative sources said. Overseas hacker involvement is also suspected, they said.
News On Japan - Nov 26
Panicked passengers on a Shinkansen bullet train were evacuated at a central Japan station on Friday night, after a plastic bag containing suspicious liquid was found onboard.
News On Japan - Nov 26
A 29-year-old man has been arrested for meeting an underage teen girl, with sexual intent, after sending her messages, promising to make her "the happiest in the world".
News On Japan - Nov 25
Inui Street, the famed autumn walk within the Imperial Palace in central Tokyo, opened to the public from Saturday.
News On Japan - Nov 25
Nissan Motor Corporation has announced plans to transition all its vehicles produced in the United Kingdom to electric vehicles (EVs).
News On Japan - Nov 25
A JR West Japan train conductor has been arrested for secretly filming eight women in the toilet of the express train "Haruka" while on duty.
News On Japan - Nov 25
Tofukuji Temple, home to 2,000 maple trees and renowned as one of Kyoto's premier autumn hotspots, features the Tsutenkyo Bridge, and the breathtaking 'sea of autumn leaves'.
News On Japan - Nov 25
The strongest cold snap of the season has brought a dramatic drop in temperatures to northern Japan, where snow began falling Friday morning, with up to 50 cm expected in Hokkaido and Tohoku by Saturday evening, and a chance of blizzards.
News On Japan - Nov 24
It's Shichi-Go-San, the Japanese festival season for celebrating the healthy growth of children, with Aibo the robot dog giving prayer at a shrine in Fukuoka, on Friday.