In all, 35 Palestinians were killed in the past two weeks, 28 during protests.
Some in the Gaza crowd threw firebombs and an explosive device, the Israeli military said.
Some rights groups maintain Israel's open-fire rules are unlawful because troops potentially can use lethal force against unarmed protesters.
As the March of Great Return continued along the Israeli border on Friday, Gaza health officials reported that Israeli forces ignored global calls for restraint and injured more than 500 Palestinians with tear gas and live ammunition, shooting at least 122 protesters.
"We want to affirm our denial of their existence on our lands by burning their flag, and call for our right of return", Said Nedal Al-majthoub, another demonstrator, told MEE.
The Ministry stated that the army targeted the clearly marked field clinics, causing seventeen medics to suffer the effects of tear gas inhalation, along with dozens of Palestinians, who were receiving treatment there.
Last week, protesters burned mounds of tyres, sending plumes of smoke into the air in the border area.
"Some people believe we are idiots to think the Israelis will allow us in, they may not, but we will not stop trying to return", said a protester, 37-year-old civil servant Ahmed, as he stood on a hilltop overlooking the Israeli fence.Like most of the 2mn Palestinians packed into the Gaza Strip, Ahmed is a descendant of refugees from Jaffa, a coastal town in Israel just south of Tel Aviv.
The apologetic letter published by The Guardian was signed by four former Israeli combatants expressing their distress over the most recent killings of demonstrators in Gaza. Israel says snipers only target the main "instigators". But Palestinians maintain protesters are being shot while posing no threat to Israeli troops.
Israeli soldiers are firing tear gas and live bullets from across the border fence.
There were also reports of clashes in the Palestinian city of Nablus where IDF soldiers were reportedly using live bullets. Since late March, 27 Palestinians have been killed and hundreds wounded by army fire during such rallies.
Today, most of the demonstrators assembled in five tent camps several hundred metres from the border fence. Smaller groups moved closer to the fence, throwing stones, torching tires and burning large Israeli flags.
Palestinian websites said a photojournalist was slightly injured in his shoulder by Israeli military fire.
The marches have been organized by Hamas, but large turnouts on two preceding Fridays were also driven by desperation among the territory's 2 million residents.
Israel alleges Hamas is using protests as a cover for attacks.
Denouncing Israel's "horrifying use of live ammunition against unarmed protesters", Mughrabi also noted that "under worldwide law, lethal force can only be used when unavoidable to protect against imminent threats to life". At the entrance, organisers had laid a large Israeli flag on the ground for protesters to step on.