The charges stem from Israel's military offensive into Gaza in December and January against Hamas militants who control the strip. Among other things, the Israeli military has been accused of using excessive and indiscriminate force in civilian areas.
Iranian President Mahmoud Ahmadinejad said Israel is "a regime that only understands the language of violence and force," CNN reported.
"I am confident that there will come a day when all Zionist criminals will be brought to justice," Ahmadinejad said on the second day of the conference in Tehran.
Israel said the offensive was an effort to end repeated rocket attacks originating from Gaza.
Israeli Foreign Ministry spokesman Yigal Palmor said the conference's claims against Israel will be heard "when this conference (starts) dealing with human rights in the countries that are members of this organization."
The two days of meetings in the Iranian capital included more than 200 senior judicial officials from the Organization of the Islamic Conference, an association of 56 states.