The aid agency says its buildings in the central part of the territory were attacked after the military targeted Deir al-Balah, which had largely been spared.
The latest deaths add to U.N. figures showing that more than 670 Palestinians have been killed since May near sites built under a new Israel-backed aid system.
Mourners at the Nasser hospital in Khan Younis, Gaza, on Saturday with the bodies of two people killed near a Gaza Humanitarian Foundation distribution site.