Twenty-four people have been charged as part of the investigation, including the head of state-owned Halkbank.
In a statement, Zafer Caglayan condemned the inquiry as an “ignoble operation”.
Prime Minister Recep Tayyip Erdogan has threatened to “break the hands” of rivals who used the inquiry to undermine his rule.
Zafer Caglayan’s son Kaan and Baris Guler, the interior minister’s son, have both denied accusations of involvement in bribery relating to urban development projects and the allocation of construction permits.
Zafer Caglayan, in his statement, said he was stepping down “so that all the light may be laid on this ignoble operation that targets our government”.
In response to the police crackdown, a number of police commissioners have been removed from their posts, including the head of police in Istanbul.
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