"A 29-year-old Palestinian died in clashes with Israeli forces in the city of Al-Khalil [Hebron] in the southern West Bank," the ministry said in a statement.
The press office of the Israeli army said the military opened fire on a man who threw a Molotov cocktail at an Israeli soldier.
"The suspect threw a Molotov cocktail at soldiers during recent riots in Hebron, endangering their lives. The soldiers returned fire and the target was hit," the military reported. The army is aware of reports of the shooting.
Palestinian Prime Minister Mohammad Shtayyeh condemned the killing of a Palestinian in the West Bank, calling it an act of "organized state terrorism carried out by the soldiers of occupation forces and settlers against our people," as quoted by Palestinian news agency WAFA.
The Palestinian Red Crescent reported that 133 Palestinians were injured in clashes with Israelis in the villages of Beita and Beit Dajan near Nablus (Shechem) on Friday.
Clashes between Israeli security forces and settlers and Palestinians protesting the occupation on the other occur almost every week in the West Bank.
Israeli settlement activity in the West Bank and in East Jerusalem, the city the Palestinian National Authority considers its capital, is a major issue in Israel's relations with the international community. Palestinians seek diplomatic recognition of their independent state on the territories of the West Bank and perceive such expansion as an encroachment on and occupation of their land.