The report alleged that hundreds of employees at almost all of Shoko Chukin Bank's offices across Japan falsified documents to make low-interest loans to firms ineligible to receive them.
The scheme was designed to lend public funds to small and mid-sized companies hurt by the 2008 global financial crisis and Japan's 2011 quake-tsunami disaster.
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Bank president Kenyu Adachi, a former high ranking industry ministry official, said he would step aside "at the appropriate time".
The private bank is about 80 per cent government-funded.
The claims "shake trust in the organisation to its core", Adachi told a press briefing.
"Top management has the biggest responsibility and I want to take that responsibility as the company's most senior executive."
Public broadcaster NHK said that Adachi will forgo his salary for six months — a common act of contrition among Japanese executives.
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