There will be "no educational activities" when the school week begins on Sunday "in light of the security situation," he said in a televised statement.
"Starting tomorrow morning and over the coming days, educational establishments, day camps, and planned trips will not take place," he said.
Israel will also limit the number of people allowed to gather outdoors to 1,000, with an even smaller number in border regions, where beaches will be closed.
There have been weekly protests in Tel Aviv and Jerusalem against the government and in favour of a hostage deal that have regularly drawn in many thousands of demonstrators.
The measures are set to last two days, according to online army guidelines.
Iran has vowed retaliation after the presumed Israeli strike on April 1 which levelled its consulate in Damascus, killing seven members of the Revolutionary Guards including two generals.
US President Joe Biden said on Friday that he expected Iran to retaliate "sooner (rather) than later".
Earlier on Saturday Iran's Revolutionary Guards seized a container ship "related to the Zionist regime (Israel)" near the Strait of Hormuz, state media reported.
Israeli Foreign Minister Israel Katz postponed a planned visit to Hungary and Austria which had been scheduled to begin on Sunday "due to the security situation," his spokesman said.
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