The ministry identified the man as Mohammed Abu Ayhour, 27, from the village of Halhul in the southern West Bank.
The Israeli military said in a statement that its troops operated in areas around the West Bank throughout Wednesday night and early Thursday. It said forces faced 'violent protests' in a number of locations, with Palestinians throwing rocks and firebombs. Troops responded to disperse the protesters using live fire and other means and nine people were arrested.
The military did not immediately respond to a request for comment on the circumstances that led to Abu Ayhour's death.
Violence has swept the region for weeks, set off by a spate of Palestinian attacks in Israel that prompted near-daily Israeli arrest raids in the West Bank. Tensions between Israelis and Palestinians were further stoked as clashes erupted in Jerusalem's Al-Aqsa mosque, and with the killing of a well-known Palestinian-American Al Jazeera journalist, who was shot covering Israeli operations in the West Bank.
The Palestinians and witnesses say Shireen Abu Akleh was killed by Israeli fire, while Israel says it's not clear if soldiers or Palestinian gunmen fired the deadly bullet.
The Palestinian attacks, which began in March and have largely subsided, killed 19 people. The Palestinian Health Ministry says more that 60 Palestinians have been killed since the start of the year. It does not differentiate between civilians, militants and those who were killed after carrying out deadly attacks.
Israel captured the West Bank, the Gaza Strip and east Jerusalem _ territories that Palestinians seek for their hoped-for state _ in the 1967 Mideast war. The West Bank is home to nearly 3 million Palestinians and has been under military rule since Israel occupied the territory.