Thousands of Palestinians had gathered for a weekly protest along Israel's border fence with the Gaza Strip, which is controlled by the Islamist group Hamas.
Gaza's Health Ministry said three Palestinians, including a 12-year-old boy, were shot dead by Israeli forces. At least 126 others were wounded by bullets, it said.
No Israelis were wounded.
Israeli army gunfire has killed at least 195 Palestinians since the border protests began in March, Gaza medics say. An Israeli soldier has been killed by a Palestinian sniper. Tracts of Israeli land have been burnt up by incendiary materials flown over the border by kite or balloon.
Israel accuses Hamas of orchestrating the protests to provide cover for attacks and distract from Gaza’s economic plight, allegations it denies. Hamas seized control of Gaza from Western-backed Palestinian President Mahmoud Abbas in 2007 and has since fought three wars with Israel, most recently in 2014.