Mojtaba Samareh Hashemi submitted his resignation, which is yet to be accepted by Ahmadinejad, on Tuesday, IRNA said.
"Allow me to submit my resignation in order to have an opportunity to serve in other areas," Samareh Hashemi said in his letter carried by IRNA.
He has been a top advisor to Ahmadinejad since he swept to power in 2005.
Ahmadinejad faces re-election on June 12 although he has yet to officially announce his candidacy.
Ahmadinejad's cabinet has gone through several reshuffles and seen key ministers sacked over differences with the president.
