Netanyahu, who was sworn in for a fifth term in May after a closely fought election, has accused the protesters of trampling democracy and the Israeli media of encouraging dissent.
Netanyahu’s right-wing Likud party called the protests “left-wing riots” and accused Israel’s popular Channel 12 news of “doing everything it can to encourage the far-left demonstrations” of the premier’s opponents.
The protesters were angry at the government's handling of the coronavirus crisis and said Netanyahu should not remain in office while on trial for corruption charges. Some of the charges he faces in a corruption trial related to alleged attempts to seek favourable coverage from media barons in return for state favours.
After moving quickly to contain the coronavirus earlier this year, critics believe Israel reopened its economy too quickly.
The country is now facing a surge in infections - confirmed cases have surpassed 82,000, including 592 deaths - while unemployment has jumped to more than 20 percent.
Self-employed workers, whose businesses have been hurt amid the economic fallout of the pandemic, also joined Saturday's protest.