The ministry says 406 demonstrators suffered other types of injuries Friday, including being hit by rubber-coated steel pellets and being overcome by tear gas.
"During our ongoing activities, the participants are asked to raise and wave Palestinian flags along with the border between eastern Gaza Strip and Israel in five different areas", he said.
According to the Gaza health ministry, since the start of the protests, over 30 Palestinians have been killed and more than 1,300 got wounds.
While the majority of the protesters have been peaceful, smaller numbers have approached Israel's border fence, throwing stones and rolling burning tyres towards troops.
"We will return to Palestine, our villages and Jerusalem", Haniyeh said in a fiery speech at one of five protest camps set up along the border.
The IDF General Staff has ordered an investigation into the Israeli military's response to the Gaza border protests.
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Friday prayers will be held outside the tents, which were erected 700 hundreds of meters away from the fence of the border. As witnessed in the past weeks, these protests have the potential to become violent.
The Israel Defense Forces referred that attacks were also carried out against "a Hamas training center" in the center of the Strip, with no victims reported so far.
Rights groups have strongly criticized Israeli forces while pointing to unverified videos that have spread online of Gazans appearing to be shot, including one seeming to show a Palestinian targeted as he ran away from the fence while holding a tire.
The marches have been organised by Hamas, but large turnouts on two preceding Fridays were also driven by desperation among the territory's two million residents.
Marchers protest contrary to a decade-old blockade and claim the things that they state is that a "right of return" of Palestinian refugees to what is now Israel.