The shootings occurred near hubs operated by the Gaza Humanitarian Foundation, which launched operations in May.
The U.S. and Israel seek to replace the traditional U.N.-led aid distribution system in Gaza, asserting that Hamas militants siphon off supplies.
Most of Saturday's deaths occurred as Palestinians massed in the Teina area, around 2 miles from a GHF aid distribution center near the southern city of Khan Younis.
Palestinians gather at a food distribution point in Gaza on Saturday.
A woman caresses a child's head as Palestinians wait at a food distribution point in the Nuseirat refugee camp in the central Gaza Strip on Saturday.
The ministry does not say how many militants are among the dead, but it says over half were women and children.
Palestinians say Israeli security forces have done little to stop the violence, and few settlers have been punished. »