Two Palestinians were killed by Israeli soldiers early on Saturday near the northern Gaza Strip town of Beit Hanun.
Details are still emerging of the clash, which took place close to the fence separating Gaza from Israel.
Meanwhile, in the West Bank city of Jenin, Israeli troops killed a 19-year-old Palestinian man and wounded two boys, local security and medical sources said.
Muhammad Salah, 19, was hit when soldiers opened fire on a group of young people throwing stones after the curfew had been imposed, the sources said.
They said the confrontation came as Israeli forces imposed a curfew on Jenin and its neighbouring refugee camp and searched homes in the area.
In the third fatal clash of the day another Palestinian, Muwataz Amudi, 15, was killed by Israeli fire in the nearby village of Birkin. Two other Palestinians were wounded as stones were being hurled at Israeli troops, Palestinian security sources and medics sources said.
The latest death brings to 3603 the number of people killed since the September 2000 outbreak of the Intifada, or Palestinian uprising, including 2688 Palestinians and 849 Israelis.
An Israeli army spokesman confirmed an operation was under way in Jenin, a bastion of the Intifada, but had no immediate comment on casualties.
“More than 20 Israeli military vehicles raided Jenin’s refugee camp on Saturday morning at 06:00 GMT,” Aljazeera's correspondent at the scene reported.
“Tens of fully armed Israeli soldiers surrounded a number of houses west of the camp and planted explosives at the front gate of one of these houses, in an attempt to track wanted activists,” he added.
One house was dynamited in the raid, after its residents had been evicted, AFP reported.
“A nine-year-old Palestinian boy was shot in his right foot by Israeli fire when he was on his way back home, as he found his school closed”
Aljazeera's correspondent in Jenin
Palestinian protestors clashed with the soldiers, throwing stones and empty glass bottles at them, and students were prevented from going to their schools.
“A nine-year-old Palestinian boy was shot in his right foot by Israeli fire when he was on his way back home, as he found his school closed,” Aljazeera's correspondent reported. “He was then taken to a hospital.”
Mayor's house occupied
Israeli forces were also reinforced in the nearby town of al-Yamoon, according to Aljazeera reports. They stormed and occupied the mayor’s house, using it as a place to interrogate Palestinians.
The army detained ten family members of the al-Aqsa Martyrs Brigades leader Ibrahim Abahra and set one of their houses ablaze, in a drive to capture the wanted resistance activist.
The raids followed similar incursions on Friday in which the Israeli army demolished three houses while attempting to capture senior Islamic Jihad member Amjad Abaidi, who is accused of planning the bombing in Haifa last month which killed 21 people.
After soldiers threw a grenade into an alleged weapons stockpile under one of the houses, Abaidi handed himself over, lightly wounded, the Israeli daily Haaretz reported.
Israelis demolished four houses in the eastern area of Jenin and while pulling out of the area killed Ahmad Shaharna, an al-Aqsa Martyrs Brigades activist, Aljazeera's correspondent reported.
Also on Friday, Israeli soldiers killed a 10-year-old Palestinian boy and three fighters in the Gaza Strip.
Arafat keeps control
Meanwhile, Palestinian President Yasir Arafat's Fatah faction backed him retaining control of security services, as Prime Minister Ahmad Quraya signalled a possible end to a power struggle with the president.
"You (Fatah) decide on the names (for a new government) and I will accept your decision"
Palestinian prime minister
"You decide on the names (for a new government) and I will accept your decision," Quraya was quoted as telling the Fatah central committee by a Palestinian official on Saturday.
Officials said Fatah - the dominant party in the Palestinian parliament - voted on Friday night for an Arafat loyalist, Hakam Balawi, to become the security chief in a new cabinet and rejected Quraya's nominee.
Fatah attempted to soften the blow to Quraya's power by appointing his man, General Nasir Yusuf, to a national security council headed by Arafat that has overarching authority over security services.
Arafat's refusal to cede security powers to his prime minister's choice is likely to anger the United States and Israel. They have attempted to sideline Arafat and Israel has accused him of fomenting violence, a charge he denies.
The power struggle between Arafat and Quraya over control of Palestinian security forces has been delaying the formation of a government and any chance of talks with Israel to revive the moribund peace "road map".
"It has also approved that the national security council headed by Arafat would be in charge of overall security," the official said. "This decision was taken while Quraya was at the meeting."
Arafat had converted Quraya's emergency cabinet into a caretaker government on Tuesday, hours before a deadline for a more permanent government, to allow time to resolve the dispute.