It was not known what other targets were hit and there were no immediate reports of casualties in the early morning air strikes.
But much of northern Gaza was plunged into darkness as the missiles knocked out electricity supplies.
The strikes came hours after two Gaza human bombers killed 10 people at Israel's port of Ashdod.
The Israeli military, which has used its helicopter fleet to track and kill scores of resistance fighters waging a Palestinian uprising in the West Bank and Gaza Strip, did not immediately comment.
But Israeli security sources said Prime Minister Ariel Sharon had convened a meeting late on Sunday night to decide on retaliation for the Ashdod attack.
Sunday's attack was jointly claimed by Hamas and al-Aqsa Martyrs Brigades, an armed wing of Palestinian President Yasir Arafat's Fatah movement.