In a televised announcement, Hanafy said much of the criticism against him was personal, in reference to reports he had been living in a posh Cairo hotel since his appointment in 2014.
"I announce, with all integrity and contentedness, that I am leaving my post," he said.
"Experience shows that being a minister is no easy task but a burden... And much of what has been said is of a personal nature."
Suppliers were found to have sold cheaper imported wheat as locally produced in order to obtain state subsidies and inflate the annual harvest, costing the government about $55 million.
The probe comes as the government seeks to cut public spending in Egypt, the world's largest importer of wheat.
Hanafy has also been accused of spending public funds on his hotel accommodation, with one member of parliament estimating the cost at USD 800,000.
Hanafy had denied the state covered his expenses, telling a newspaper he had paid for the hotel from his own pocket.
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