Gaza's civil defence agency said three aid workers were killed in an Israeli air strike in the Hamas-run territory on Saturday but the Israeli army said it killed a "terrorist."

The agency said the aid workers killed were Palestinian employees of World Central Kitchen. The US aid group did not immediately respond to requests for comment.

The Israeli army said it had "struck a vehicle with a terrorist that took part in the murderous October 7 massacre," referring to the militant group Hamas's unprecedented attack on Israel last year.

"The claim that the terrorist was simultaneously a WCK worker is being examined," it added in a statement.

Civil defence agency spokesman Mahmud Bassal said the bodies of "at least five dead were transported (to hospital), including (those of) the three employees of World Central Kitchen."

"All three men worked for WCK and they were hit while driving in a WCK jeep in Khan Younis," Bassal said, adding that the vehicle had been "marked with its logo clearly visible."

The Israeli army insisted its strike in the main southern city hit "a civilian unmarked vehicle and its movement on the route was not coordinated for transporting of aid."

In April, an Israeli air strike killed seven WCK staff – an Australian, three Britons, a North American, a Palestinian and a Pole.

Israel said it had been targeting a "Hamas gunman" in that strike but the military admitted a series of "grave mistakes" and violations of its own rules of engagement.

The October 2023 attack resulted in the deaths of 1,207 people, most of them civilians, according to a tally of Israeli official figures.

Israel's retaliatory military offensive has killed 44,382 people in Gaza, according to figures from the territory's health ministry which the United Nations considers reliable. (AFP)