"The terrorist act… should be condemned by the international community," Mekdad said, commenting on the incident during his meeting with Iranian Ambassador to Syria Javad Torkabadi.
He warned there is a risk of tensions in the Middle East intensifying after Fakhrizadeh's killing.
"The UN should fulfil its obligations concerning countering terrorism and stick to the norms of international law, otherwise we will achieve only increased tensions in the region," Mekdad added.
On Friday, Fakhrizadeh, an Iranian nuclear physicist and the head of the Iranian Defense Ministry's innovation center, was killed in a gunmen attack in the town of Absard in the Tehran region. Iranian Foreign Minister Mohammad Javad Zarif accused Israel of being involved in the death of the nuclear scientist, and called on the international community to condemn the act. On Saturday, Iranian President Hassan Rouhani said that the crime would not go unanswered.