It said five passersby were wounded, one was in a critical condition.
"The dead were taken to a local hospital literally piece by piece," Dr. Muavia Hasanen, head of the Health Ministry Emergencies Department, told a RIA Novosti correspondent.
At least 13 people have been killed in Israeli air strikes on Gaza, the majority of them activists of an armed wing of the governing Hamas movement.
The Israeli Air Force Thursday attacked the headquarters of a special purpose unit of the Palestinian Interior Ministry, purportedly controlled by the Hamas movement and manned by Islamist militants.
At least two people were killed and 20 injured, while the building was completely destroyed, local television said citing eyewitness accounts.
The Israeli government said earlier it had abandoned its policy of 'restraint' toward Palestinian militants and pledged to retaliate against rocket attacks from Gaza, as fighting continues between Palestinian factions.
Israeli forces earlier launched missiles at a Hamas base following rocket fire, and reporters were trapped by gunfire in Gaza City.