Saudi authorities have not issued visas for the Iranian participants, ministry spokesman Abbas Mousavi said.
"The government of Saudi Arabia has prevented the participation of the Iranian delegation in the meeting to examine the 'deal of the century' plan at the headquarters of the Organization of Islamic Cooperation," Mousavi said, the Fars news agency reported.
Mousavi said Iran has filed a complaint with the OIC and accused Saudi Arabia of misusing its position as the host for the organization's headquarters. There was no immediate comment from Saudi officials.
Iranian officials have condemned Trump's plan for resolving the conflict between Israel and Palestine as a non-starter after it was officially announced last week. The Palestinian leadership has rejected the plan, saying it heavily favors Israel and will deny them a viable independent state.
Saudi Arabia and Iran are locked in a proxy war as they vie for influence across the Middle East. They support opposite sides in the conflicts in Syria and Yemen.