At least 83 people were hospitalised in Gaza, the ministry said in a statement, as thousands again demonstrated along the heavily fortified border.
It did not say how many of those were gunshot wounds but three people were reported to be in critical condition.
Numbers were lower than recent Fridays, however, an AFP correspondent said.
A spokeswoman for the Israeli military said some 10,500 Palestinians were taking part in the events, some of whom were throwing stones at soldiers.
At least 263 Palestinians have been killed by Israeli fire since the protests and clashes began a year ago.
Two Israeli soldiers have been killed over the same period in Gaza-related violence.
Five men were killed on Saturday as tens of thousands gathered for the first anniversary of the protests.
Israel says its strong response is necessary to defend its borders and accuses Hamas, the Islamist movement that rules the Gaza Strip, of orchestrating violence there.
A February United Nations report accused Israeli soldiers of intentionally firing on civilians, saying it could amount to war crimes.
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