"This is a clear signal that the IOC is not accepting any kind of discrimination," IOC President Thomas Bach said.
The IOC opened an investigation after the head of the Israeli Baseball Association, Peter Kurz, was told he could not display the Israeli flag or Israeli name plate at the World Baseball Softball Confederation congress in Hammamet, Tunisia, in May.
The IOC executive board noted that the WBSC had taken its own "appropriate and reasonable" punitive measures, suspending the Tunisian federation for six months.
But the IOC said it was warning the world body "to ensure that a similar situation is not repeated in the future."
The IOC said the measure was taken "in view of the critical importance of maintaining respect for all members of the Olympic movement and upholding the Olympic values at all times."
Kurz was one of 150 delegates from 90 nations attending the congress in Tunisia. He said he was asked to sit without his national flag or sign "for my own wellbeing and for the sake of the host country." He filed a complaint to the WBSC.
"We examined it and understood it was probably a lower-level person, it wasn't a plot," Anita DeFrantz, an IOC executive board member from the United States, told The Associated Press. "It seemed someone individually took an initiative, but nevertheless it's inappropriate, and we want to make sure the organization understood the responsibility for ensuring that the Olympic movement's principle is applied."
The warning is an embarrassment for the WBSC, which was recently formed to merge the two sports as part of a joint bid to win inclusion in the 2020 Tokyo Olympics. Baseball and softball have been out of the Olympics since the 2008 Beijing Games and have failed in several attempts to secure reinstatement.
"It's not necessarily a blow to anything that will happen to that federation in the future but ... this is a signal they have to be proactive and make sure it does not happen again," said Christophe Dubi, IOC deputy executive director of the Olympic Games.
In October 2013, Tunisia's tennis federation ordered the country's top player to withdraw from a match against an Israeli opponent at a tournament in Uzbekistan. Malek Jaziri had been scheduled to play Israel's Amir Weintraub in the quarterfinals of an ATP challenger in Tashkent. He withdrew before the match and Weintraub advanced to the semifinals of the lower-tier event.