The ministry said the victim, identified as Mohammed al-Jabari, 24, was shot during clashes between Israeli forces and Palestinian protesters in the southern West Bank city of al-Khalil (Hebron) on Friday. He later succumbed to his injuries in hospital.
The official Palestinian news agency Wafa said the man had disabilities, without elaborating.
The Israeli military claimed that the slain man intended to hurl a firebomb at the soldiers.
Rights groups have denounced Tel Aviv’s extrajudicial killings in situations where they say alleged assailants could have been detained in a non-lethal manner. Hundreds of Palestinians have been killed in similar circumstances.
According to the Palestinian human rights group Jerusalem Legal Aid and Human Rights Center (JLAC), Israel is currently holding the bodies of 19 Palestinians killed in the past two years, along with 260 bodies of those killed since 1967.
The occupied Palestinian territories have witnessed a new wave of tension ever since US President Donald Trump announced his decision on December 6 last year to recognize Jerusalem al-Quds as Israel’s "capital" and relocate the US embassy in Israel from Tel Aviv to the occupied city.
Israel occupied the West Bank and East Jerusalem al-Quds during the Six-Day War in 1967. In a move not recognized by the international community, the regime later annexed East Jerusalem al-Quds, which is sought by Palestinians as the capital of their future state.