Hamas's armed wing, the al-Qassam Brigades, handed over the remains of the three hostages to the Red Cross on Sunday night after saying they had been found "along the route of one of the tunnels in the southern Gaza Strip".
The bodies were transferred to Israeli forces in Gaza before being transported to the National Centre of Forensic Medicine in Tel Aviv for identification.
On Monday morning, the Israeli prime minister's office announced that the remains belonged to Col Hamami, Capt Neutra and Staff Sgt Daniel.
"The government of Israel shares in the deep sorrow of the Hamami, Neutra and Daniel families, and all the families of the deceased hostages," a statement said.
"The Hamas terrorist organisation is required to uphold its commitments to the mediators and return them as part of the implementation of the agreement. We will not compromise on this and will spare no effort until we return all of the hostages, every last one of them," it added.
Col Hamami was commander of the Southern Brigade of the Israel Defense Forces (IDF) Gaza Division. The IDF said the father-of-three was among the first troops to reach the combat zones following the Hamas-led attack on southern Israel on 7 October 2023 and was "the first to declare war". He was killed fighting near Kibbutz Nirim and his body was then taken to Gaza by Hamas as a hostage, it added.
Capt Neutra, an Israeli-American dual national who was born in the US and emigrated to Israel, was serving as a platoon commander in the IDF's 7th Brigade. The IDF said he was killed in battle near the Gaza perimeter and that his body was abducted by Hamas.
Staff Sgt Daniel was serving in the IDF's 7th Armoured Brigade. He was also killed during a battle with Hamas gunmen near the Gaza perimeter and his body was taken by them as a hostage, according to the IDF.
The Hostages and Missing Families Forum in Israel, which represents many hostages' relatives, said it "bows its head in sorrow and shares in the profound grief" of the three men's families.
"There are no words to express the depth of this pain. The hostages have no time. We must bring them all home, now!"