Israeli Apache attack helicopters fired two missiles at the headquarters of the Palestinian interior ministry in Gaza City.
No casualties were reported and the ministry building was empty at the time of the air strike late on Thursday, said Palestinian eyewitnesses, adding that the building was set on fire and sustained severe damages.
The interior ministry is headed by senior Hamas member Saeed Siam.
Meanwhile, Israeli military planes fired another two missiles at an office in downtown Gaza City, which belonged to the al-Aqsa Martyrs Brigades, an armed wing of Palestinian President Mahmoud Abbas' Fatah movement, said witnesses.
Some damages were caused to the building but there was no report of any casualties.
The Israeli army has confirmed the two strikes.
On Thursday, they pressed ahead a broad ground operation into the Gaza Strip in a bid to rescue an Israeli soldier kidnapped by Palestinian militants on Sunday.
In addition, Palestinian security sources said two missiles hit an area near the only power plant in the Gaza Strip early Wednesday, causing no casualties.
The power plant was destroyed in the Israeli air raid, leading to a blackout in most areas of the Gaza Strip.
The operation, launched Wednesday, is the first of its kind since Israel withdrew troops and settlers from the Gaza Strip nearly a year ago after 38 years of occupation.