Ibrahim Abu Thurayeh, a 29-year-old whose family said had lost his legs in a 2008 Israeli strike, was shot in the head by a sniper during protests and clashes along the Gaza border on December 15, according to the health ministry in Gaza.
The United Nations' human rights chief said he was "truly shocked" by Abu Thurayeh's death and demanded an "independent and impartial investigation".
On Thursday, Israel's military announced it was opening a probe into his death, after previously saying it was not able to determine whether he had been killed by its soldiers' fire.
"As stated previously, the IDF's (Israel Defence Forces) operational review concluded that no live fire was aimed at Abu Thurayeh," it said in a statement.
"Based on the information gathered during the review, it was not possible to determine whether Abu Thurayeh was injured as a result of riot dispersal means or what caused his death.
"In order to further examine the case, including information received from organisations operating in the Gaza Strip, it was decided that the circumstances of (Abu) Thurayeh's death will also be examined by a military police investigation."
AFP photographers have seen Abu Thurayeh at multiple demonstrations in recent years.
In video footage recorded the day he was killed, Abu Thurayeh could be seen carrying the Palestinian flag and waving the victory sign at Israeli soldiers across the border.
The protest on December 15 was part of unrest that has occurred in the Palestinian territories since US President Donald Trump's recognition of Jerusalem as Israel's capital.
Fourteen Palestinians have been killed since Trump's December 6 announcement, most of them in clashes with Israeli forces
Source: AFP
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