The IOC said it was also cutting off all discussions about any potential Olympic Games bid by Indonesia until the government provided assurances that all athletes, irrespective of nationality, would be eligible to compete there in future.
In a statement, the IOC said: "...All eligible athletes, teams and sports officials must be able to participate in international sports competitions and events without any form of discrimination from the host country, in accordance with the Olympic Charter..."
Indonesia has expressed an interest in hosting the 2036 Summer Olympics.
Indonesia, the world's largest Muslim-majority country, denied visas to Israeli gymnasts earlier this month amid an outcry over Israel's military offensive in Gaza, meaning they could not take part in the World Artistic Gymnastics Championships that began last week in Jakarta.
The Israel Gymnastics Federation called Indonesia's decision shocking and heartbreaking.
Indonesia has no formal diplomatic ties with Israel.
