Salah Helal was arrested shortly after the Egyptian cabinet released a statement saying that his "resignation has been accepted" upon a request by President Abdel-Fattah El-Sisi.
Several agriculture ministry officials are being investigated on corruption allegations, state-run Al Ahram reported.
The resignation stemmed from Helal's alleged "involvement in a corruption case," the report said without providing details.
In August, the assistant and director of the agriculture minister's office was arrested and accused of corruption and receiving bribes from businessmen to facilitate the allocation of state land.