Tear gas and smoke are pictured through a window during a large-scale Israeli military raid in the old town of Nablus city
The military said troops opened fire and killed two Palestinians.
The Palestinian health ministry said authorities had been informed by Israel of the deaths of Nidal Amira, 40, and Khaled Amira, 35. It did not specify whether the two were related.
AFPTV footage showed Israeli soldiers standing in one of the old city's narrow streets, next to two dead bodies.
An AFP journalist said dozens of military vehicles entered Nablus's historic centre shortly after midnight (2100 GMT Monday).
At a major square outside the old city, young men and boys gathered on Tuesday to burn tyres and throw stones at the Israeli armoured vehicles.
The Palestine Red Crescent Society said that during the Israeli raid, at least three people were injured from bullet shrapnel, four from "physical assault", and dozens more from tear gas inhalation.
It added that ambulances were blocked from entering the old city, obstructing the work of medical teams.
Israel said in a statement that its forces had searched "250 structures" and arrested "six" during Tuesday's operation.
The northern West Bank, where Nablus is located, has been the target of a major Israeli offensive since late January.
Israel has occupied the West Bank since 1967 and its forces regularly carry out raids that authorities say target Palestinian militants.
An AFP correspondent in Nablus saw Israeli soldiers searching shops and detaining several people on Tuesday.
The correspondent said Israeli flags were raised over the roofs of buildings taken over by the troops and used as temporary bases.
The old city of Nablus has seen several major Israeli raids, including in 2022 and 2023 during large-scale operations targeting a local grouping of armed fighters, and in 2002 during the second Palestinian intifada, or uprising.
Violence has surged in the West Bank since the start of the Israeli war on Gaza.
The Palestinian Authority says at least 938 Palestinians have been killed in the West Bank by Israeli soldiers or settlers since October 2023.
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