Abdelraouf Salhah was shot in the head during the protest, as was 43-year-old female activist Amal al-Taramsi who died on Friday. Two dozen Palestinians were also wounded, said the ministry’s statement.
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Salhah was the third Palestinian to be pronounced dead since Friday’s protest in the besieged territory.
An estimated 13,000 Palestinians took part in Friday’s demonstrations, an Israeli military spokesman said.
“The rioters have burned tyres and hurled blocks, explosive devices and grenades towards (Israeli) troops and at the Gaza Strip security fence,” an army spokeswoman said.
Another Palestinian, Anwar Quday, 33, died on Saturday of wounds from protests and clashes three weeks ago. The besieged enclave’s health ministry said he was shot in the neck.
Hamas has been orchestrating weekly mass protests along the perimeter fence since March last year to protest an Israeli-Egyptian blockade imposed on Gaza for nearly a decade.
More than 240 Palestinians have been killed since the protests began and thousands of others have been wounded. An Israeli soldier was also killed.
Most of the Palestinians killed during the demonstrations were shot in weekly clashes, but others have been hit by Israeli tank fire or air raids.
Israel says it’s protecting its border from infiltrators who could carry out attacks.