The family of the boy, Khalid Walwil, said he was shot in the head on Saturday morning when Israeli forces opened fire at the family home, according to Aljazeera's correspondent.
The family said the child had been standing at the window of his home and just turned his back when he was shot and killed.
An Israeli military commander told reporters that there was no Israeli gunfire at the time of the incident, although troops had fired at Palestinian resistance fighters in earlier fighting.
The boy died of his wounds on the way to hospital after occupation troops blocked the way of the ambulance transporting him.
Israeli troops also occupied three houses in the refugee camp during the raid.
Palestinian youths are reported to have thrown stones at the troops' military trucks.
The Israeli troops then fired live rounds, hitting the six-year-old Palestinian, sources said.
The Israeli forces say they were searching for a resistance activist suspected of being behind a number of attempts in recent weeks to smuggle explosives.