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Gaza's health ministry also reported that 408 Palestinians had been taken to hospitals and medical centres for treatment. The dead included a 16-year-old, it said.
At least six journalists were shot and wounded, according to a statement from the Palestinian Journalists Syndicate. A spokeswoman for the Israeli army had no immediate comment on the statement.
Palestinians burned mounds of tyres and threw stones at Israeli soldiers over the border fence, who responded with tear gas and live fire.
Israel said there were also attempts to break through the barrier. Thousands of protesters -- Israel estimated 20,000 -- gathered in locations near the border east of Khan Yunis, in the south of the blockaded Palestinian enclave, and east of Gaza City, among other spots.
The number of protesters, however, was lower than last week, when a demonstration by tens of thousands led to clashes in which Israeli forces killed 19 Palestinians on March 30.
Hamas's leader in Gaza, Yahya Sinwar, hailed the protests and condemned Israel's blockade of the Gaza Strip.
"They said Gaza would give up its principles, its project of liberation and (dream) of return if they starve it, but Gaza is coming out today," he said to protesters east of Khan Yunis.
He referred to the protest's call for Palestinian refugees to be able to return to land they fled or were expelled from what is now Israel.
Sinwar said Gazans would "break the border and return to our land and pray in Jerusalem." Israel's military said "attempts were made to infiltrate into Israel under the cover of a smoke screen."
It also said explosive devices and firebombs were thrown, adding that soldiers opened fire "in accordance with the rules of engagement."
Israeli army spokesman Brigadier General Ronen Manelis defined the day's events as a success. "None of our troops were wounded, the border was not crossed," he said, noting that what happened last week had "deterred Hamas, which prevented the masses from approaching the (border) fence."
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Mona al-Shaar, 43, who was distributing bottles of vinegar to protesters east of Khan Yunis to dab onto tissues to help them cope with tear gas said. "We came here for the land and for a better future."
"The Israelis are cowards." Israel had warned that its open-fire rules would remain unchanged for Friday's protest, pledging to stop damage to the fence and prevent infiltrations or alleged attacks.
It had faced mounting criticism over its use of live fire, and UN chief Antonio Guterres called for restraint ahead of the new protest. "I particularly urge Israel to exercise extreme caution with the use of force in order to avoid casualties," he said.
Kuwait on Friday called on the UN Security Council, to back an independent inquiry on the Israeli-Palestinian clashes, a week after a vain attempt to do the same thing.
"It's a matter the Security Council should address," said Kuwait's UN ambassador Mansour al-Otaibi. The text brought by Kuwait, a non-permanent member of the Security Council, is the same as the one it submitted earlier which was blocked by Washington.
The Palestinian UN ambassador Riyad Mansour said that if the UN does nothing it "is encouraging Israel" in its operations against Palestinians. If the Security Council fails to act then the Palestinian side could take the issue to the wider UN General Assembly, he added.
Meanwhile the Palestinian representative in Washington warned Friday that the situation in Gaza was explosive and that the region cannot afford to wait for the promised new US peace plan.
Israel accuses Hamas, the Islamist movement that runs the Gaza Strip and with whom it has fought three wars since 2008, of using the protests as cover to carry out violence.
Israel says more than half of the dead from the previous Friday were members of militant groups, including the armed wing of Hamas.
Hamas's armed wing has claimed only five of them, saying they were participating "in popular events side-by-side with their people."
Militant group Islamic Jihad has claimed at least one of the dead as a member. Hamas has meanwhile offered compensation of $3,000 to the families of protesters killed and $500 for those seriously injured, drawing outrage from Israel.
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The protests in support of refugees are designed to last six weeks. More than 700,000 Palestinians fled or were expelled from their lands during the war surrounding Israel's creation in 1948.
Israelis say allowing the so-called "right of return" would mean their country would cease to exist.
The White House on Thursday refrained from criticism of Israel and called on protesters to remain peaceful.
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