"60 people were injured by (Israeli) occupation forces" and of these 36 were shot by live fire, ministry spokesman Ashraf al-Qudra told AFP.
An Israeli army spokeswoman said approximately 7,000 "rioters and demonstrators" had gathered in multiple spots along the heavily-fortified border.
Demonstrators "hurled rocks and a number of explosive devices" towards troops, she said, with forces responding in "accordance with standard procedures".
Palestinians in Gaza have for more than a year gathered at least weekly along the border for often-violent protests, calling on Israel to end its blockade of the enclave.
At least 264 Palestinians in Gaza have been killed by Israeli forces since the protests began.
The majority were killed during clashes, with others hit by tank fire or air strikes.
Two Israeli soldiers have been killed over the same period.
Two million Palestinians live in impoverished Gaza, crammed between Israel, Egypt and the Mediterranean.
Israel, which has fought three wars with Hamas, has blockaded the enclave for more than a decade, and Egypt often closes Gaza's only other gateway to the outside world.
Agencies contributed to this report.
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