Israel rejected calls for an independent probe on Sunday after its soldiers killed 16 Palestinians and wounded hundreds more when a major demonstration led to clashes along the border with the Gaza Strip.
Israel's military has faced questions from rights groups over its use of live fire on Friday, the bloodiest day in the conflict since a 2014 war, while Palestinians accuse soldiers of firing on protesters posing no threat.
Both UN Secretary-General Antonio Guterres and EU diplomatic chief Federica Mogherini have called for an independent investigation.
On Saturday, the United States blocked a draft UN Security Council statement urging restraint and calling for an investigation of the violence, diplomats said.
Prime Minister Benjamin Netanyahu praised soldiers' actions for "guarding the country's borders," while Defence Minister Avigdor Lieberman said the protests were not a "Woodstock festival."
Lieberman said calls for an independent investigation were hypocritical and on Sunday repeated his rejection of such an investigation.
"There will be no commission of inquiry," he told Israel's public radio.
"There will be no such thing here. We shall not cooperate with any commission of inquiry."
Netanyahu also hit back at Turkish President Recep Tayyip Erdogan over his sharp criticism of what he called Israel's "inhumane attack" in Gaza.
"The most moral army in the world will not be lectured to on morality from someone who for years has been bombing civilians indiscriminately," Netanyahu tweeted.
He has previously labelled Erdogan as someone who "bombs Kurdish villagers."
The protest, which includes tents erected at various areas, is designed to last six weeks, ending around the time the United States moves its embassy from Tel Aviv to Jerusalem in mid-May.
The embassy move has deeply angered the Palestinians, who see Jerusalem's annexed eastern sector as the capital of their future state.
But while tens of thousands attended Friday's start of the protests, demonstrations have since dwindled. Several hundred attended on Saturday, while on Sunday dozens milled around protest tents.
The protests may however again see large crowds after Friday's main Muslim prayers and for upcoming key dates.
May 14 will mark 70 years since the creation of Israel and is when the United States is expected to open its new Jerusalem embassy.
Palestinians will mark what they call the Nakba, or "catastrophe," the following day.
The Nakba commemorates the more than 700,000 Palestinians who either fled or were expelled from their homes in the war surrounding Israel's creation in 1948.
Gaza's protest is in support of refugees, including those in the Palestinian enclave who want to return to their former homes in what is now Israel.