At least 83 people were hospitalized in Gaza, the ministry said in a statement, as thousands again demonstrated along the heavily fortified border, AFP reported.
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, the report added.
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.
Five men were killed last Saturday as tens of thousands gathered for the first anniversary of the protests.
A February United Nations report accused Israeli soldiers of intentionally firing on civilians, saying it could amount to war crimes.