"In addition, the incident will be examined by the General Staff Fact Finding Assessment Mechanism, and the findings passed to the Military Advocate General", for a separate determination on whether criminal proceedings should be initiated, he added.
The leaflets reportedly warned Gazans "to refrain from participating in demonstrations and chaos, which will only endanger your lives".
Israeli war planes threw flyers over Gaza city on Thursday afternoon, warning the people there not to join Friday's protests and rallies in eastern Gaza Strip.
Palestinian medics said that at least 120 Palestinians have been killed since the start of the popular return marches on the borders between the Gaza Strip and Israel on March 30, with nearly daily clashes on the border.
The Israeli military controls most of the territory of the West Bank, protecting 400,000 Jewish settlers who now live there among around 3 million Palestinians. Hamas leaders have threatened possible mass border breaches, raising concerns in Israel that communities near Gaza might be at risk.More news: North Korea-US summit scheduled for morning of June 12: White House
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Israel and Egypt argue that they must maintain the blockade to contain Hamas and other militant groups, which have built weapons arsenals over the years, including short-range rockets. Al-Quds is the historic Arabic name for Jerusalem, and Iran says the day is an occasion to express support for the Palestinians.
Chanting "Death to Israel", demonstrators protested Israel's occupation of Jerusalem, the city where Muslims believe Islam's Prophet Muhammad began his journey to heaven.
Participants thinned since the largest protests coinciding with the opening of the new USA embassy in Jerusalem last month, however Israel is gearing up for a larger turnout on Friday. Israel's current government has said it will not accept a partition of the city as part of a peace deal with the Palestinians. USA -brokered peace talks collapsed in 2014.
Police also detained two other Palestinians, including a youth, from inside the courtyards of Al-Aqsa Mosque compound. The compound sits on the ruins of biblical temples and is revered by Jews as the holiest site of their religion.
Associated Press writers Ian Deitch in Jerusalem, Ariel Schalit in Kibbutz Nahal Oz and Amir Vahdat in Tehran contributed.