In a statement, the ministry published the names of 10 victims, which include an old man, a teenager and eight members of the Palestinian militant group known as the Lions' Den.
In addition, 102 Palestinians, including three local journalists, were injured by Israeli soldiers during the four-hour clash in the Palestinian city, with six of them in critical condition, according to the statement.
Israeli Army Leaves 6 Dead and Over 30 Wounded in the West Bank
Thousands of Palestinians gathered in front of the three main hospitals in the city, where the dead and wounded were accommodated, and chanted slogans against Israel.
In separate statements, Palestinian factions declared a general strike on Thursday to mourn those killed in Nablus, calling on the Palestinians to confront the Israeli forces all over the West Bank.
Local sources and eyewitnesses said the clash broke out when an Israeli force backed by armored vehicles stormed the outskirts of the old city of Nablus and surrounded a house to arrest several Palestinians wanted by Israeli army.
They said the wanted Palestinians were armed and exchanged fire with the soldiers, adding several explosions and gunfire were heard in the entire city.
Meanwhile, in the city's streets, dozens of Palestinians threw stones and empty bottles toward the soldiers, who fired back to disperse them.
The Israeli military said in a statement that the raid aimed at arresting suspects for the killing of a soldier near an Israeli settlement last year, adding no injuries were reported among its soldiers.
Meanwhile, Palestinian Prime Minister Mohamed Ishtaye condemned the Israeli killing.
"The Israeli aggression is an organized terrorism through which Israel seeks to export its internal crisis to the Palestinian arena," he said.
"Whatever is practised against our people will not deter them from continuing their legitimate struggle to achieve their goals of freedom, ending the occupation, and establishing their independent state, with Jerusalem as its capital," the prime minister added.
In Gaza, Abu Obeida, military spokesman of Al-Qassam Brigades, the armed wing of the ruling faction Hamas, said in a short statement that "the patience of the Palestinian resistance in Gaza is running out."
The tension between Israelis and Palestinians has been flaring since early January in the West Bank.
Israeli forces killed at least 61 Palestinians since the beginning of 2023, mainly during daily raids allegedly aimed at arresting suspects in deadly Palestinian attacks, according to the Palestinian health ministry. Meanwhile, official figures from Israel showed 11 Israelis have been killed in Palestinian attacks since the beginning of 2023.