Carders have made off with US$12.7 million (£8.7 million, A$17.5 million) ripping through 1400 ATMs in a mere two hours last week.
The attackers netted ¥1.4 billion in cash from ATMs located in convenience stores across the country using counterfeit credit cards.
Sources told local media the 1600 credit cards used in the attacks contained account information from an unnamed South African bank.
Tokyo is working with South African police through INTERPOL to investigate the theft and bank breach, Mainichi.jp reports.
Up to 100 people are thought to have hit the ATMs across 16 prefectures including Kanagawa, Osaka, Aichi, and Fukuoka in the early hours of 15 May in what amounted to a staggering 14,000 transactions.
ATMs belonging to Japan's Seven Bank (part of the Seven Eleven convenience store group) were fleeced of the maximum withdrawal amount of ¥100,000 (US$910, £627, A$1,255).
Police are examining CCTV footage and have placed a Malaysian group on an international watch list.
Carder gangs often employ teams of footmen to hit ATMs in coordinated raids. In one recent large-scale attack, hackers compromised 30 banks credit cards to rip $200 a minute from ATMs across Russia.
The crims compromised the bank network to roll-back transactions while other crooks emptied ATMs. ®