Monday's strike came hours after Ehud Olmert, the Israeli prime minister, ordered the military to intensify its operation to free a captured Israeli soldier.
The Israeli army said the latest strike targeted a meeting place in Gaza City for militants from the al-Aqsa Martyrs Brigades - a group linked to president Mahmoud Abbas's Fatah movement.
It was unclear if there were any casualties.
Witnesses also reported two missiles landing in open areas in northern Gaza, near the town of Beit Lahiya.
Late on Sunday, Israeli soldiers shot dead three Palestinian fighters in a confrontation in the southern Gaza Strip, the Israeli army and medics said.
The clashes occurred at Gaza's disused international airport where Israeli forces have been deployed since an incursion last week in a bid to free a soldier captured by Palestinian fighters during a cross-border raid.
Witnesses who live near Dahaniya, the site of the airport, said they heard gunfire and an explosion after darkness fell.
An Israeli military spokeswoman said soldiers opened fire on three men who approached them armed with guns and explosive belts, and that all three died of their wounds.
"I have given instructions to intensify the strength of action by the army and security services," Olmert said at a cabinet meeting on Sunday.
"Everyone understands that giving in to terror today means an invitation to the next act of terrorism, and we will not act that way."
On Sunday Israeli aircraft attacked the empty office of the Ismail Haniya, the Palestinian prime minister.