Witnesses said soldiers fired on Palestinians throwing stones at them in the city of Nablus, killing a 16-year-old boy.
Adli Yaaish, head of the Nablus municipality, told Aljazeera that the Palestinians were injured by rubber-coated as well as live bullets in the raid at 1.30am on Saturday.
The witnesses said protesters threw stones after the army surrounded a building where two wanted al-Aqsa Martyrs Brigades fighters were believed to be holed up.
Aljazeera's correspondent said Israeli bulldozers demolished the four-storey building which housed about 100 people, after the two refused to surrender.
Yaaish said the soldiers forced residents of the building out and interrogated them.
The Israeli army said it would not comment because the operation had not ended.
Israeli troops also detained four Palestinians in the Gaza Strip near the southern town of Rafah, residents said, adding that those taken away were not fighters.
An army spokeswoman said two militants from the governing Hamas movement had been detained.
Residents said two Palestinians were wounded by gunfire in that operation.