More than 90 others were injured in the strike on Al-Mawasi camp, the ministry said, condemning a "brutal massacre."
It came as the Israeli military pursued attacks in central Gaza with artillery fire and drone strikes heard by an AFP correspondent, while Palestinian medics said one bombing killed a father and his three daughters.
Palestine Red Crescent medics said the strike on a home in Deir al-Balah city killed Rital al-Raey, five, Mai, eight, Leila, nine and their 40-year-old father Mohammed al-Raey.
Their bodies were taken to the city's Al-Aqsa hospital, the medical workers said.
AFPTV images showed ambulances arriving at the hospital with wounded. One man carried the apparently lifeless body of a child, whom he placed on the floor beside others.
An AFP correspondent in the Palestinian territory, under Israeli military retaliation since the October 7 attack by Hamas militants on Israel, reported artillery shelling in southeast Gaza City and the al-Rimal district in the city centre.
The correspondent reported drone strikes at Tal al-Hawa in the southwest of Gaza's main city.
The Civil Defence agency in Hamas-run Gaza said Friday that Israeli forces had withdrawn from Tal al-Hawa and other districts, after days of fighting. It said at least 60 bodies had been found in Tal al-Hawa and a neighbouring area after the withdrawal.
On Thursday, the agency said 60 bodies had been found in nearby Shujaiya after Israel ended an operation there. Israel's military said it had killed 150 militants in Shujaiya during a two-week operation against Hamas.
On Saturday the army said operations were continuing in Gaza City as well as "targeted, intelligence-based" missions in Rafah in the south of the Gaza Strip.
It said "numerous" tunnels had been destroyed in the Rafah area, and "multiple" Hamas militants killed.
Also in Rafah, the military said it struck a paraglider storage facility used by fighters in the unprecedented October 7 attack during which some militants used the aircraft.
The October 7 Hamas attack resulted in 1,195 deaths, mostly civilians, according to an AFP tally based on Israeli figures. The militants also seized 251 hostages, 116 of whom remain in Gaza, including 42 the military says are dead.
Israel's military reprisal has killed at least 38,345 people in Gaza, also mostly civilians, according to data from Gaza's health ministry.
