Israel's air force launched on Saturday a number of simultaneous airstrikes targeting the ruling radical Islamist movement Hamas's paramilitary units.
The ministry said in a press release that 140 bodies and around 300 injured people had been brought to hospitals in Gaza. Doctors said the number of victims was unprecedented.
"I wouldn't even try to count the injured," local health authority spokesman Moawiya Hassanain said earlier.
According to preliminary information, most of the injured are members of Hamas or the Gaza police controlled by the Islamist movement, which runs the Palestinian enclave on the Mediterranean.
After the bombing, the streets of Gaza became flooded with students trying to get home.
"There is complete chaos," said one resident, who was trying to find her daughter, a student. "No one can find anyone and the phone networks are not working."
Israeli Prime Minister Ehud Olmert issued a personal "last-minute" appeal to Palestinians in Gaza on Thursday to stop rocket fire at Israel and promised to use "Israel's might" to strike Hamas.
"I say to you in a last-minute call, stop it," Olmert said in an interview with the Arab TV station Al Arabiya, adding: "I will not hesitate to use Israel's might to strike Hamas and [Islamic] Jihad."
On Wednesday, Palestinian militants fired over 40 rockets and 20 mortar shells at southern Israeli border towns in the largest daily attack since the end of a six-month ceasefire in Gaza six days ago.
Hamas seized control of the Gaza Strip from President Mahmoud Abbas's Fatah group in June 2007.
