The Israeli military confirmed it had hit a camp on Saturday, used by resistance fighters affiliated with the Fatah group of Mahmoud Abbas, the Palestinian president.
Palestinian witnesses said the Abu el-Reesh Brigades, an armed wing of Fatah, had used the camp to train their fighters.
Medics said the strike killed six people and injured two.
Also on Saturday, an Israeli air strike killed two al-Aqsa Martyrs Brigades fighters, also part of Fatah.
An Israeli army spokesman said: "We identified a cell from the al-Aqsa Martyrs Brigades firing rockets into Israel. They fired the rockets, they got into the car and we hit the car."
Two people were wounded, one critically, in the strike on the car in the outskirts of the Shijaia neighbourhood of Gaza City.
The attacks took place a day after an Israeli missile killed five fighters and one of the fighter's five-year-old son.
Hamas vows retaliation
Israel has stepped up air strikes and artillery barrages on Gaza in recent days in response to rocket fire from Gaza, from which Israel withdrew last year after 38 years of occupation.
The makeshift rockets from Gaza rarely cause casualties.
The armed wing of Hamas, the Islamist group that formed the Palestinian government last week after winning parliamentary elections in January, said there would be retaliation.
The armed wing of Hamas has largely abided by a 14-month-old truce and kept a lid on its rhetoric in recent months.