Ihab al-Ghusain, a spokesman for the Hamas Executive Force, said the violence started when members of the Heles clan opened fire at the security forces.
The security forces later arrested a number of "outlaws" that were on their way to send reinforcements to the clan, al-Ghusain said.
A Fatah official, speaking on condition of anonymity, said Hamas security forces were trying to confiscate a car that belonged to a Heles member.
Residents said the sound of ambulances could be heard throughout Gaza City following the incident. Armed clashes often break out along factional and family lines across the Gaza Strip.