UN High Commissioner for Human Rights Zeid Ra'ad Al Hussein welcomed an investigation launched by the Israeli military into the death of Ziad Abu Ein in the West Bank on Wednesday.
He said the probe needed to be "quick and utterly transparent if people are to have faith in its findings".
"Peaceful protest is a human right and security forces must exercise appropriate restraint when policing protests in accordance with international standards," he added.
"Because of the well-established illegal nature of the Israeli settlements in the West Bank and East Jerusalem, such protests will inevitably continue."
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Abu Ein was pronounced dead after the confrontation with Israeli soldiers, which occurred during a march against settlements by about 300 Palestinians who intended to plant olive trees as a symbolic act.
The Palestinian leadership blamed Israel for "killing" the 55-year-old, while Israeli authorities said an investigation had been launched and called for calm.
The UN rights chief also urged a "proper" investigation into the shooting on Wednesday by Israeli troops of a 14-year-old Palestinian boy during a clash at the Jelazoun refugee camp in the West Bank.
He drew attention to a sharp rise in reports of excessive use of force by Israeli forces in the occupied territories, noting at least 50 Palestinian fatalities in the West Bank in such circumstances so far this year -- almost double the 27 that occurred in 2013.
"This continuous stream of fatal incidents underscores the need for effective accountability measures," Zeid said.