"The Islamic Republic of Iran deeply regrets this disastrous mistake," he wrote on Twitter. "My thoughts and prayers go to all the mourning families. I offer my sincerest condolences."
The investigation will continue, Rouhani wrote in a separate tweet.
All 176 people aboard the airliner were killed in the crash shortly after takeoff.
(Reporting By Babak Dehghanpisheh; Editing by Shri Navaratnam)