Fakhrizadeh, a nuclear physicist who headed the ministry's research and innovation unit, was assassinated earlier in the day, as confirmed by the ministry. The physicist was attacked along with his bodyguards by a group of unknown assailants in the Absard city not far from Tehran and died from wounds later in the hospital.
"We will come upon the killers of this innocent martyr like a thunder and make them regret what they did," Dehghan said, as quoted by Iran's Mehr news agency.
Like Iranian Foreign Minister Mohammad Javad Zarif, Khamenei's adviser believes that Israel was behind the assassination.
As reported by Iranian news agency Fars, the attack involved shooting and at least one explosion.
There previously were multiple instances when Iranian nuclear scientists were targeted in direct assassination attempts. Many in Iran believe they were carried out by the Israeli intelligence force Mossad. Although Israel has neither confirmed nor denied this, Israeli officials have repeatedly vowed to seek that Iran stops its nuclear program.