The university professors said the agriculture ministry had ignored key aims outlined by state development plans such as "food security, strengthening of public purchasing power and controlling inflation".
"Unfortunately, despite the long-term plans, the current policies of the government and the wrong executive methods of the agriculture ministry have been working in the opposite direction," the Sarmayeh newspaper quoted the letter as saying.
The letter, signed by 54 agriculture professors from across the country, blamed the ministry’s "one-dimensional plans to focus on wheat production and put pressure on water sources, which have led to increases in the retail price of beans, meat and dairy products".
"These have weakened people’s purchasing power and thus caused a severe lack of nutrition in society."
In October, Agriculture Minister Mohammad Reza Eskandari survived a motion in the conservative-controlled parliament to impeach him.
A group of MPs accused the minister of falsifying reports to cover up failures as fruit imports increased in the world’s eighth fruit producer.
They also accused him of "laying off experienced staff and making appointments based on family contacts" and the ministry of being "ignorant of the country’s self-sufficiency plans".
Ahmadinejad however has defended his minister’s performance.