Nine deaths were reported, as well as a large number of injuries at contested crossing points along the West Bank, Gaza, Syrian and Lebanese borders.
The New York Times reported the worst confrontation took place in the Golan Heights where hundreds of Palestinians living in Syria broke through a border fence and poured into the village of Majdal Shams where troops opened fire, killing four people.
The coordinated marches came on the annual Nakba observance, which marks the establishment of Israel in 1948 and is considered a day of mourning among Palestinians.
In Lebanon, hundreds of buses were organized to transport Palestinians to the country's southern border with Israel, al-Akhbar reported. Israel Radio said Lebanese troops were deployed in southern Lebanon to prevent Palestinian protesters from reaching the Israeli border.
In Gaza, thousands of Palestinians marched toward the Erez border crossing. The army said it was investigating Palestinian claims that more than 40 protesters were injured by Israeli soldiers, Israel Radio said.
Israeli Defense Minister Ehud Barak said on Channel 2 the border breaches are emblematic of the more complex situations the military will have to handle in the future, Haaretz reported.
"The [military] must protect the sovereignty of Israel and it succeeded in doing so," Barak said, adding investigations will be conducted into the violent confrontations "so that lessons can be learned."
"There were deaths there in several places and we regret the deaths," he said. "Those responsible for this are those who attempted to violate Israel's sovereignty and those who sent them, if there are any."
Ynetnews reported Palestinian President Mahmoud Abbas said during a speech Sunday "the blood of the Nakba fatalities was not spilled in vain. They died for the Palestinian people's rights and freedom."
Abbas said Palestinians "can feel their state coming together and that the world supports the end of Israeli occupation," Ynetnews said.
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