The 18 were hit with live ammunition as a few thousand gathered in different spots along the heavily-guarded border line, the ministry said.
None were reported to be in life-threatening condition. Palestinians in Gaza have since March 30, especially on Fridays, held often violent protests backed by the strip's Islamist rulers Hamas.
Gaza fishermen struggle to survive amid Israel's maritime restrictions
Numbers have dwindled since a ceasefire agreement between Hamas and Israel earlier this month after a flare-up. At least 235 Palestinians in Gaza have been killed since March, mostly by Israeli fire during border clashes but also by air and tank strikes.
Two Israeli soldiers have been killed over the same period, one by a Palestinian sniper and another during an aborted special forces operation inside Gaza.
Israeli gunfire kills 2 Gaza border protesters: Palestinians
Protesters are calling for Palestinian refugees to be allowed to return to their former homes now inside Israel. Israel accuses Hamas of seeking to use the protests as cover to carry out infiltrations and attacks, and says the army actions are necessary to defend the border.
Israel has fought three wars with Hamas since 2008.
Around 6,000 Palestinians have been shot by Israeli forces over the past eight months, according to the health ministry. Doctors Without Borders (MSF), which has provided care for Palestinians since the protests began, warned this week that Gaza's healthcare system is being overwhelmed by the high number of casualties.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ