The man was shot during the protests which are held weekly near the village of Nabi Saleh.
The man was shot during the protests which are held weekly near the village of Nabi Saleh, north of Ramallah, and later died in a nearby hospital, the ministry said in a statement.
The dead man was named as Saba' Nidal Obaid, 20.
The Israeli army said in a statement to AFP it was "aware of reports" that a protester had been killed but could not confirm it.
"A violent riot involving dozens of Palestinians hurling rocks at (Israeli army) forces broke out earlier today," a spokeswoman said.
"Dispersal means," including firing live ammunition, were used "in response to that imminent threat".
A wave of unrest which erupted in October 2015 has claimed the lives of 263 Palestinians, 41 Israelis, two Americans, one Jordanian, an Eritrean, a Sudanese and a Briton, according to an AFP count.
Most of the Palestinians killed were carrying out knife, gun or car-ramming attacks, Israeli authorities say.
Others were shot dead during protests or clashes, while some were killed in Israeli air strikes on the Gaza Strip.