The Israeli military issued evacuation orders on Sunday in areas of central Gaza packed with displaced Palestinians in Deir al-Balah, while medics said 94 people were killed waiting for aid as hunger mounts.
The military evacuation demand signals an imminent attack on neighbourhoods in the area.
The ministry said dozens of people were also wounded in the incident in northern Gaza, in one of the highest reported tolls among repeated recent cases in which aid seekers have been killed. Other people were killed near another aid site in the south, it said.
In total, health authorities said 88 people had been killed by Israeli gunfire and airstrikes across Gaza on Sunday.
After Israel's military dropped leaflets urging people to evacuate Deir al-Balah's neighbourhoods, 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.