A separate Israeli air strike on Tuesday hit a school run by the UN agency for Palestinian refugees (Unrwa) in Nuseirat that was housing displaced people.
The Gaza health ministry said 23 people were killed, and photographs show extensive damage of the building.
The IDF statement said it had struck “terrorists” who were operating in the school and directing attacks on its troops in Gaza.
“Prior to the strike, numerous steps were taken in order to mitigate the risk of harming civilians, including the use of aerial surveillance, precise munitions, and additional intelligence,” it added.
The IDF accused Hamas of exploiting civilian buildings and using civilians as human shields, which the group has denied.
This is the sixth school across Gaza that Israel has hit in 10 days, attacks that UN officials have strongly condemned.
Two people were reportedly killed in another strike in Nuseirat on Tuesday afternoon, while strikes in the camp overnight left four people dead.
The IDF said on Tuesday morning that it had struck about 40 “terror targets” across Gaza over the previous day.
It also said that troops had killed fighters and dismantled tunnel shafts during a continuing ground operation in the southernmost city of Rafah.
Also on Tuesday, the military wing of Palestinian Islamic Jihad fired rockets into Israeli territory near Gaza for the first time in two weeks, hitting the town of Sderot. One person was reported lightly injured while running for shelter.
