Israeli forces responded with riot dispersal methods and said it was firing in accordance with the rules of engagement.
At least 41 protesters have been killed by Israel fire since the protests began in late March - with some estimates going as high as 53.
The same source said 167 people were wounded.
The slain man identified as the 40-year-old Jabr Salem Abu Mustafa was protesting east of Khan Younis in southern Gaza on Friday, the Palestinian Health Ministry reported.
The Nakba will be protested with various activities - which will take place in the West Bank, the Gaza Strip and in Arab villages inside Israel - including seminars, marches and protests, according to organizers from the National Committee for the Commemoration of the Nakba.
Demonstrations this week were once again met with violence from Israeli forces who fired live ammunition, rubber bullets and tear gas canisters at protesters participating in the Great March of Return.
Israeli snipers and spotters have been seen along the border, with live rounds being used to repel protesters.
3 critically hurt in attack on South Africa mosque ahead of Ramadan
South Africa has a history of relative religious tolerance. "It was a sudden attack and at this point we don't have enough information".
The Gaza Strip, home to 2 million people, is run by the Islamist group Hamas which has fought three wars against Israel in the past decade.
Rioters near the border fence with Israel reportedly threw grenades, pipe bombs, and rocks at soldiers.
It has accused Hamas of using the protests as a cover to attack the border, insisting it has a right to protect it.
With the expected opening of the U.S. Embassy in Jerusalem on Monday, Israeli and American flags are being displayed on several main streets.
Thousands of Indonesian Muslims stage a rally protesting US President Donald Trump's recognition of Jerusalem as Israel's capital.
Since the rallies began some six weeks ago, at least 48 Palestinian demonstrators have been martyred and hundreds more - possibly thousands - injured.