The United States ambassador to the United Nations, Nikki Haley, has defended Israel for its “restraint” in dealing with protests that left at least 60 Palestinians dead in violent clashes with the military.

Thousands of Gaza residents turned out for the funerals of loved ones killed by Israeli troops on Tuesday as protests over the opening of the new US embassy in Jerusalem resulted in the bloodiest day for Palestinians since the 2014 Gaza conflict.

Among the dead from shooting or tear gas was an eight-month-old baby who died from tear gas that her family said she inhaled at a protest camp.

Two more Palestinians were killed overnight in separate shootings in Gaza, while Palestinian medical authorities said more than 2200 protesters had been injured by gunfire or tear gas.

The Israeli army estimated that more than 40,000 Palestinians took part in the protests at a dozen sites along the border fence, and said its soldiers were following “standard operating procedures” to push back people seeking to break through the border fence.

At a special meeting of the United Nations Security Council on Wednesday morning (AEST), Ms Haley denied the violence in Gaza was a response to the new US embassy, saying the blame laid with the Palestinian Hamas party.

“Who among us would accept this type of activity on your border? No one would,” Ms Haley told the UN.

“No country in this chamber would act with more restraint than Israel has,” she said.

Ms Haley said the opening of the US embassy in Jerusalem “does not undermine prospects for peace in any way”.

“Those who suggest that the Gaza violence has anything to do with the location of the American embassy are sorely mistaken. Rather, the violence comes from those who reject the state of Israel in any location,” she said.

The UN Middle East peace envoy Nikolay Mladenov said there was “no justification” for the Israeli response and called the protesrs a “day of tragedy.”

He urged the international community to refrain from taking unilateral action that steers Israel and Palestine away from the peace process.

International criticism has poured down on Israel for its use of force on the border, with Belgium, Ireland and Turkey all summoning their Israeli ambassadors.

Turkish broadcasters said the Israeli top envoy was told “return to Tel Aviv for a while”.

State broadcaster TRT said the ambassador was being told to leave.

In an apparent tit-for-tat, Israel then requested the Turkish consul general in Jerusalem leave the country.

The moves fall short of formal expulsions but come after Turkish President Recep Tayyip Erdogan said Israel committed “genocide” in killing dozens of Palestinians along the Gaza border.

Demonstrators took to the streets in South Africa in solidarity with Palestinians on Wednesday morning, with anti-apartheid icon Archbishop Desmond Tutu declaring himself “broken-hearted” over the violence.

In a phone call with Israeli Prime Minister Benjamin Netanyahu, French President Emmanuel Macron denounced the killing of civilians and urged Israel to protect civilians and allow peaceful protest, according to a source close to the Elysee Palace.

German Chancellor Angela Merkel showed understanding for Israel’s security interests in a call with Mr Netanyahu, but stressed that the violence should not be a means to achieving political goals, her spokesman Steffen Seibert said.

The move comes after the US on Tuesday blocked the adoption of a joint UN Security Council statement calling for an independent investigation.

In Geneva, the UN human rights office condemned what it called the “appalling deadly violence” by Israeli forces and said it was extremely worried about what might happen later.

-with AAP