While Saudi authorities put the death toll at 717, Iranian Hajj officials say nearly 1300 pilgrims died in the stampede during Hajj pilgrimage rituals in Mina on Thursday.
More than 125 of the victims were Iranian nationals.
The Supreme Leader in his message declared three days of national mourning.
Ayatollah Khamenei said the disaster created a “great grief” in the Islamic world.
The Leader instructed Iran’s Hajj and Pilgrimage Organization and his representative office in Makkah to continue their efforts to help the Iranian pilgrims and extend all possible assistance to the pilgrims of other countries.
Ayatollah Khamenei also referred to the role of mismanagement in the incident, saying, “The Saudi government is obligated to shoulder its heavy responsibility in this bitter incident and meet its obligations in compliance with the rule of righteousness and fairness.
“Mismanagement and improper measures that were behind this tragedy should not be overlooked,” the Leader went on to say.