While Israel would like to amplify the impacts of its actions against Iran, Khamenei said on Sunday, adding it would also not be right for Iran to dismiss the strikes as insignificant, CNN reported.
"They're making a miscalculation concerning Iran," he said in comments published on his website.
"They still haven't been able to correctly understand the power, capability, ingenuity, and determination of the Iranian people. We need to make them understand these things."
Khamenei said that those who believe Iran should avoid producing weapons to avoid provoking backlash are misguided.
Keeping a country weak does not maintain its security, he added.
The Iranian leader also condemned Israel's military offensive in Gaza, as well as the international community for enabling them, CNN reported.
"War operates within a framework of rules, laws, and limitations. These limitations can't just be disregarded during a war. However, the criminal gang ruling over the occupied lands has trampled all boundaries and rules underfoot," he said.
Both Iranian and Israeli officials appeared deliberate on Saturday in their initial framing of Israel's retaliation for Tehran's major missile attack earlier this month.
Israel's public posture immediately after the strikes was relatively muted. That was intentional, a source familiar with the Israeli government's thinking said, aimed at allowing Iran to downplay the strikes and avoid further escalation.
Iran's government seemed to seize that opportunity, claiming the strikes caused only limited damage at military sites, even as it acknowledged that four Iranian soldiers were killed.