According to the ministry, the shooting took place in connection with clashes with Israeli soldiers in a Palestinian refugee camp in the southern West Bank.
The Israeli military announces that people who threw stones at vehicles on a road near the refugee camp were fired upon.
“(Soldiers) saw the suspects adjacent to the refugee camp... and responded by opening fire on them.
A hit was identified," the military writes in a statement.
Multiple fatal shootings
Wednesday's incident comes a day after an Israeli soldier was shot dead in the northern West Bank.
The perpetrator has not been arrested in that case and a manhunt for the suspect is underway.
The Israeli security forces are also looking for a perpetrator who shot dead an Israeli soldier in East Jerusalem on Saturday.