The loans in question, mostly auto loans, were made through Orient, which has pledged to end them.
Mizuho said an in-house probe had found that transactions with "anti-social elements" were known about in early 2011 and reported to some senior executives, contrary to earlier statements that the information had not been shared to topmost management.
But the problems were set aside at the time as the bank scrambled to deal with ATM malfunctions triggered by an influx of donations for victims of the 2011 tsunami disaster.
The troubles at Mizuho underscore the difficulties financial companies confront in avoiding dealings with those deemed to be affiliated with organized crime and are reinforcing calls for more data sharing by police and financial institutions.
Japanese gangs, known as "yakuza," have long been involved in many areas of the economy, despite efforts to freeze them out of the financial system.