"The air force carried out an attack on a weapons storage facility containing Qassam rockets and mortars in the town of Beit Hanoun," a military spokeswoman said in Jerusalem.
Residents said the missile struck a water pumping station on Wednesday. There were no immediate reports of injuries.
Israel has stepped up air activity in Gaza recently in response to rocket and mortar bomb attacks by Palestinian resistance fighters on Jewish settlements and a town in southern Israel.
In the hours leading to the air strike, Palestinians fired more than 20 rockets and mortar bombs at Gaza settlements.
They say the attacks are retaliation for Israeli raids to capture wanted fighters.
Last Wednesday, an Israeli aircraft fired missiles at four Islamic Jihad members in the Gaza village of Beit Lahiya as they launched rockets into Israel. No one was hurt but a rocket was destroyed.
Islamic Jihad says Israel is still
trying to kill its members
An Israeli government official said before last week's missile strike that Israel could stage air attacks in Gaza, even at the risk of civilian casualties, to ensure its planned pullout from the occupied territory did not come under fire.
Suspected weapons depots and workshops, frequently targeted by Israel during the past four years of violence with the Palestinians, have not been hit from the air since the truce was announced.
Meanwhile, Islamic Jihad's Secretary General in Cairo, Ramadan Shallah, held talks on Wednesday with Egyptian Intelligence Chief Omar Sulaiman, Aljazeera's correspondent in Egypt reported.
The meeting concentrated on the latest developments in the occupied territories, particularly Israeli attacks against Islamic Jihad activists in Gaza.
Shallah reiterated Islamic Jihad's commitment to the Cairo agreement with other Palestinian factions, and its right to retaliate for Israeli violations of the "period of calm", sources told Aljazeera.
In another development, Israeli soldiers have stormed into Yatta village, near al-Khalil (Hebron) and taken over a number of Islamic charity societies and houses, Aljazeera's correspondent in al-Khalil reported.
The Israeli force began a search operation after erecting military check points.
The raid comes after an Israeli settler was killed a few days ago by Palestinian fighters near the Bait Hajai settlement, south of Hebron.
Israeli soldiers are reported to
have invaded Hebron
And in Ram Allah, the president of the European Parliament has said he has discussed with Israeli and Palestinian officials the idea of convening a meeting for parliamentarians from the European Union and the Middle East by the end of the year.
Addressing the Palestinian Legislative Council in Ram Allah on Wednesday, Joseph Fontaine stressed the importance of this meeting in pushing forward the peace process in the region.