It said an air strike had been anticipated and personnel had been evacuated from the five-story structure days before.
Palestinian radio also reported an Israeli air strike against a naval police command post in central Gaza. No casualties have so far been reported.
Earlier on Friday, Israeli soldiers killed two Palestinian gunmen during military operations in the Gaza Strip and the West Bank, Palestinian radio said.
One of the gunmen was killed in an air strike on north Gaza during which three others were wounded. All of the fighters belonged to the hard-line Islamic group Hamas, which has controlled the enclave of 1.5 million since June, the reports said.
Another fighter, a field commander of the al-Aqsa Martyrs Brigade, a paramilitary group affiliated to Fatah, was shot dead by Israeli soldiers in the West Bank.
Seven Palestinians, including a mother and child, were killed in Israeli air strikes on Gaza on Thursday. The fighting escalated on Tuesday when an Israeli raid on Gaza killed 19 people. A total of 34 Palestinians have been killed by Israeli troops in the past three days.
Gaza militants fired at least six rockets into Israeli territory on Thursday, slightly injuring an Israeli woman, the Israeli military said.