The military launched a surprise attack in the city on Monday after issuing immediate evacuation orders for residents in its eastern neighborhoods.
At least 129 people have since been killed and over 400 others injured in the area, which was previously designated as a “safe zone” for displaced people by the Israeli army.
A joint statement by the army and the Shin Bet domestic security service claimed the bodies of the hostages were located in Khan Younis on Wednesday.
According to the statement, the five were killed during a Hamas attack into southern Israel on Oct. 7, 2023, and their bodies were taken to Gaza.
There are still around 115 Israelis held captive by Hamas in Gaza, according to Israeli media.
There has been no comment from Hamas on the Israeli statement. The Palestinian group earlier announced that some 70 hostages had been killed in Israeli attacks on the enclave.
Israel, flouting a United Nations Security Council resolution demanding an immediate cease-fire, has faced international condemnation amid its continued brutal offensive against Gaza since an Oct. 7, 2023 attack by the Palestinian resistance group Hamas.
At least 39,100 Palestinians have since been killed, mostly women and children, and over 90,000 injured, according to local health authorities.
Over nine months into the Israeli onslaught, vast tracts of Gaza lie in ruins amid a crippling blockade of food, clean water and medicine.