More than 922 people were taken to hospitals and field clinics, the ministry said, but did not provide a breakdown of those injured by live fire, rubber-coated steel pellets or overcome by tear gas.
It said 19 people were in serious condition.
Thousands of protesters – Israel estimated 20,000 – gathered in locations near the border east of Khan Yunis, in the south of the blockaded Palestinian enclave, and east of Gaza City, among other spots.