The captain of a cruise liner carrying more than 200 passengers and crew members died in an apparent accident on Sunday, the authorities said.
The Israeli ship, the Captain Elia, lost power shortly after leaving the port of Ashdod, the ministry said.
The vessel’s captain, who was a member of the crew, and seven crew members suffered non-life threatening injuries, it said in a statement.
The ship was not carrying any passengers or crew, it added.
The captain, an Israeli national of Palestinian origin, was the second crew member on board to die in the past week.
The ship’s first passenger, a Palestinian woman, died of injuries she suffered in the accident.
Last month, a group of Palestinians and Israeli soldiers clashed at a checkpoint in the Gaza Strip.
Israel has been trying to curb the smuggling of Gaza’s coastal enclave, which has been under an international blockade since 2007, with an intensified military campaign, and Israel says it will enforce the restrictions with all possible force.
Israel also says it is carrying out the blockade to stop rockets being fired from the Gaza strip toward the territory.
The Gaza Strip, however, has seen several flare-ups in recent months, as militants in Gaza, including Hamas, and the Islamic Jihad group, have been seeking to exploit the blockade in an attempt to gain ground.
The two sides have been locked in a deadly conflict in the coastal enclave since 2007.
The conflict has killed more than 2,000 Palestinians and more than 5,000 Israelis, mostly civilians.
Israel’s Iron Dome missile defense system has intercepted more than 3,000 rockets fired from Gaza since the blockade began, and hundreds of Israeli civilians have been killed.