A second airstrike, several hours after the first strike early on Sunday, targeted a bridge near the northern Gaza town of Beit Hanoun that Palestinian fighters used to gain access to rocket-launching sites, the Israeli military said.
Palestinian security officials and witnesses said the two missiles that were fired landed in an empty field near the border with Israel, and the Israeli military said it couldn't confirm the missiles hit their target.
The three fighters killed in the first strike were senior Al Aqsa field operatives, the hospital said. Field operatives plan and carry out rocket attacks and other assaults on Israeli targets.
Some of the dead and wounded were pulling away in a car from the targeted building when a missile struck, leaving their vehicle an unrecognisable heap of charred and twisted metal.
Four of the wounded were security personnel guarding Preventive Security headquarters near the Al Aqsa facility, the hospital said.
The Israeli military said the strike was meant to deter rocket attacks on Israel from the Gaza Strip, such as one that wounded an Israeli baby and two adults in a kibbutz in southern Israel on Friday.
After that attack, claimed by Islamic Jihad fighters, and another one Friday in which rockets landed near the city of Ashkelon, Israel also fired dozens of artillery rounds at northern Gaza and eastern Gaza City.
The Israeli military said the facility targeted in the first airstrike served as a training camp for Al Aqsa operatives, and as a rocket- and mortar-launching site. Palestinians said it was an Al Aqsa sports club and sports training camp.
"God willing, our rockets, our self-sacrificing martyrs and all the means of resistance will chase out the Zionists from every corner of our occupied land"
Al Aqsa member
The car that was hit was travelling on a small street between the Al Aqsa facility and Palestinian Preventive Security offices.
Dozens of Al Aqsa members and supporters of the affiliated Fatah Party gathered outside the hospital after the airstrike, some firing rifles in the air outside the morgue.
One Al Aqsa member, who identified himself as Abu Mujahed, accused Israel of carrying out a targeted killing of the group's fighters, but the Israeli military denied that.
"God willing, our rockets, our self-sacrificing martyrs and all the means of resistance will chase out the Zionists from every corner of our occupied land," Abu Mujahed said. "God willing, our revenge will come by deeds, and not by words."