In comments at a press conference on Sunday, Alireza Refiepour said the bird flu would have spread to many parts of the country if the culling operation had not taken place.
According to the official, 15 provinces in Iran witnessed the outbreak of avian flu.
He also noted that arrangements have been made to secure a steady supply of chicken and eggs, saying the Agriculture Ministry even imported eggs to balance the market.
A hike in the price of chicken eggs in Iran over the past month forced the administration to import the product from abroad. Officials blamed bird flu for a shortage of eggs in the market.
Avian flu, a type of influenza caused by viruses adapted to birds, has also broken out in some other countries lately, including in Britain and Turkey.