"I take this opportunity to send condolences to the families of the 66 civilians that lost their lives in the plane accident today," Netanyahu said at the Munich Security Conference.
"We have no quarrel with the people of Iran, only with the regime that torments them," he added.
Earlier in his fiery speech, the premier warned Tehran not to "test Israel's resolve" as tensions between the arch enemies have reached fresh heights over Iran's activities in Syria.
Officials said an Iranian passenger plane on a domestic flight crashed into the country's Zagros mountains today, killing all 66 people on board.