The Israeli military said it struck a group of Palestinians who launched incendiary balloons from southern Gaza into Israel on Sunday.
According to a report in Gaza, the airstrike hit east of Rafah, a refugee camp and city in the southern Gaza Strip.
The attack comes two days after Gaza authorities said three Palestinians, one of them a teenage boy, were killed by live Israeli fire during a protest at the Israel-Gaza border.
Those killed were identified by Gaza's Health Ministry as 12-year-old Faras Assarsawei, 24-year-old Mahmud Abu Sma'an and 28-year-old Hussein Fathi Arkab.
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The Israeli military said some 20,000 Palestinians took part in the protests, adding that protesters hurled hand grenades and explosive devices toward troops, and set tires on fire and rolled them toward soldiers.
The IDF said it struck twice in northern Gaza during the protest in response to attacks by Palestinian demonstrators.
The Israeli military announced Thursday that it was going to bolster its troops along the Gaza border in the coming days over concerns that the protests will escalate.
The Israeli army is also preparing for the option that rockets will be fired on Gaza-border communities in the coming days, which could lead to a wider confrontation. Iron Dome missile defense batteries have been deployed in several areas to ward off the threat.