An Israeli army spokeswoman said that two Islamic Jihad fighters were shot and killed on Friday when they resisted arrest and shot at soldiers from within a cave where they were hiding.
The shooting occurred near the West Bank city of Bethlehem.
Later on Friday, Israeli troops also fired at a group of Palestinians near Gaza's border with Israel, killing one fighter and wounding a second, Palestinian medical officials said.
Palestinian security officials said the men were members of Islamic Jihad.
The group confirmed that a 19-year-old member was killed.
The army said it fired at two Palestinians who were engaging in "suspicious activity" near Gaza's border fence with Israel.
Also on Friday, three Palestinians from the armed wing of the governing Hamas movement died in the West Bank city of Jenin while they were preparing a bomb, local security officials said.
The Izz el-Deen al-Qassam Brigades described the men as engineers, the term it uses for bomb-makers.
Earlier, an Israeli air strike destroyed a building in the Gaza Strip where the army said armed groups were making rockets, wounding at least one.
Violence has continued in the West Bank and Gaza Strip while Israel has also been fighting Hezbollah in Lebanon. A five-day-old ceasefire in the war in Lebanon has largely held.
The current Israeli offensive in the Gaza Strip, which aims to recover a captured soldier and stop cross-border rocket fire, has so far killed about 180 Palestinians.