Mohammad-Reza Eskandari had been accused of incompetence and mismanagement of the Agriculture Ministry.
Earlier this month, more than 50 Majlis deputies signed a statement calling for Eskandaris impeachment.
The motion was brought before Majlis for an official vote. A total of 242 deputies took part in the vote, of which 98 filed blank ballots. The exact number of ayes and nays were not immediately announced.
Eskandari, 47, was a founding member of Jihad Sazandegi, affiliated to the Islamic Revolutionary Guards Corps.
