The Ministry said dozens of people were also wounded in the incident in northern Gaza. It was one of the highest reported death tolls among repeated recent cases in which aid seekers have been killed, including 36 on Saturday. Another six people were killed near another aid site in the south, it said.
Israel's military said its troops had fired warning shots towards a crowd of thousands of people in northern Gaza on Sunday to remove what it said was "an immediate threat".
It said initial findings suggested reported casualty figures were inflated, and it "certainly does not intentionally target humanitarian aid trucks".
It did not immediately comment on the incident in the south.
The United Nations (UN) World Food Programme (WFP) said that shortly after entering Gaza, a WFP convoy of 25 trucks carrying food aid encountered "massive crowds of hungry civilians" who then came under gunfire.
"WFP reiterates that any violence involving civilians seeking humanitarian aid is completely unacceptable," it said in a statement.
In total, health authorities said 88 people had been killed by Israeli gunfire and airstrikes across the enclave on Sunday.
DISPLACED GAZANS EVACUATE
After Israel's military dropped leaflets urging people to evacuate from neighbourhoods in central Gaza's Deir al-Balah, residents said Israeli planes struck three houses in the area.
Dozens of families began leaving their homes, carrying some of their belongings. Hundreds of thousands of displaced Gazans have been sheltering in the Deir al-Balah area.
Israel's military said it had not entered the districts subject to the evacuation order during the current conflict and that it was continuing "to operate with great force to destroy the enemy's capabilities and terrorist infrastructure in the area".
Israeli sources have said the reason the army has so far stayed out is because they suspect Hamas might be holding hostages there. At least 20 of the remaining 50 hostages in captivity in Gaza are believed to still be alive.
Hostage families demanded an explanation from the army.
"Can anyone (promise) to us that this decision will not come at the cost of losing our loved ones?" the families said in a statement.
ACCELERATING STARVATION
Much of Gaza has been reduced to a wasteland during more than 21 months of war and there are fears of accelerating starvation.
Palestinian health officials said hundreds of people could soon die as hospitals were inundated with patients suffering from dizziness and exhaustion due to the scarcity of food and a collapse in aid deliveries.
"We warn that hundreds of people whose bodies have wasted away are at risk of imminent death due to hunger," said the health ministry, which is controlled by Hamas.
The UN also said on Sunday that civilians were starving and needed an urgent influx of aid.
Pope Leo called for an end to the "barbarity of war" as he spoke of his profound pain over an Israeli strike on the sole Catholic church in Gaza that killed three people on Thursday.
--Reuters--