Ibrahim Abu Thurayeh died on December 15 during protests and clashes along the Israel-Gaza border against US President Donald Trump's controversial recognition of Jerusalem as Israel's capital.
His family says he had lost his legs in an Israeli strike a decade earlier.
Israel's military said earlier this month it was opening an investigation into the death of the 29-year-old after previously saying it was not able to determine whether he had been killed by its soldiers' fire.
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The justice ministry in Gaza announced Sunday his body had been exhumed and on Monday a commission affiliated to Gaza's militant rulers Hamas said he had been shot by Israeli forces.
Emad al-Baz, from the organisation which Hamas tasks with gathering evidence about alleged Israeli crimes, told a news conference that multiple tests had been conducted on the body, including X-ray scans.
"The autopsy revealed the bullet entered above his left eye and stayed in his head."
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El-Baz said the autopsy indicated the bullet was fired from some 30 metres (yards) away, the distance between protesters and the Israeli army.
The United Nations' human rights chief has said he was "truly shocked" by Abu Thurayeh's death and demanded an "independent and impartial investigation".
Seventeen Palestinians have been killed since Trump's December 6 announcement, most of them in clashes with Israeli forces. One Israeli has been killed in that timeframe.
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