An Israeli military spokeswoman confirmed the air strike and said it was in response to the frequent firing of rockets and mortar bombs by fighters into nearby Israeli towns.
In another development in the coastal territory, Hamas security officials said they arrested a Palestinian who was set to detonate a bomb at a gathering hosted by Ismail Haniyah, a Hamas leader, for returning Hajj pilgrims on Saturday afternoon.
Ehab al-Ghsain, spokesman for Hamas's Executive Force, said security men caught a suspect with 4kg of explosives ready to be detonated by cellular phone at a rally where Haniyah welcomed home hundreds of pilgrims.
"The investigation is taking several directions [to discover] whether the aim was to assassinate Haniyah, or to kill as many people as possible," al-Ghsain said.
Another security official accused Fatah of being behind the plot. A Fatah official in the West Bank rejected the allegation as "fabrications and lies".
Ziad abu al-Enain in Ramallah said: "Since Hamas stole the authority in the Gaza Strip it has only been practicing lies and deception."
Earlier on Saturday, unidentified gunmen stormed the American International School in the Gaza Strip, smashing windows, seizing computers and torching buses but causing no injuries, security sources said.
In a leaflet left behind after the attack, the gunmen claimed affiliation with al-Qaeda and vowed to attack other symbols of "immorality" throughout the coastal territory.
The school is a private Palestinian institution that is part of an association of "American Schools" in the Middle East.
Hamas's interior ministry said in a statement: "An investigation was immediately launched into the attack and we will pursue and bring the attackers to justice regardless of their motives."