The Israeli military recovered the bodies of some 51 hostages during the two years of the Israel-Hamas war in the coastal territory.
Netanyahu called the return of body parts a "clear violation" of the US-brokered ceasefire agreement by Hamas.
There are still 13 bodies of hostages in Gaza, and the slow recovery of those remains is posing a challenge to implementing the next stages of the ceasefire.
Hamas has said it is struggling to find the bodies amid the vast destruction in Gaza, while Israel has accused the militant group of purposely delaying their return.
Earlier on Tuesday, Israeli authorities said they had killed three Palestinian militants early during an operation in the northern part of the occupied West Bank, the latest action in Israel's stepped-up military activity in the territory since the October 7, 2023, Hamas attack that triggered the war in Gaza.
Israeli police said the three men were shot as they came out of a cave near Jenin, a town in the northern West Bank known as a militant stronghold.
The Israeli military said the militants "took part in terror activity in Jenin", but gave no further details.
Two militants where shot and killed in the initial volley of gunfire, and the third, who was wounded, was killed shortly after, according to the Israeli military.
An earlier statement said the Israeli military carried out an air-strike shortly afterward to destroy the cave.
The army confirmed an air strike in the area but gave no further details.
Hamas condemned the Jenin strike but did not identify the slain men as Hamas members.
Israel says its operations have cracked down on militants in the West Bank.
But Palestinians and human rights groups say scores of uninvolved civilians have also been among the dead, while tens of thousands of people have been displaced from their homes.
The ceasefire in Gaza has been holding since it began on October 10.
In exchange for the returned dead hostages, Israel has handed back to Gaza 195 Palestinian bodies, fewer than half of which have been identified.
On Monday, 41 unidentified bodies were buried in the Gaza city of Deir al-Balah and a funeral was held in Israel for the slain hostage Yossi Sharabi, whose remains were returned earlier this month.
At the weekend, Egypt deployed a team of experts and heavy equipment to help search for the bodies of hostages still in Gaza.
That work continued on Monday in Khan Younis.
The last 20 living hostages were returned to Israel when the ceasefire began, and in exchange Israel freed roughly 2000 Palestinian prisoners.
Most of those freed were seized in Gaza by Israeli troops during the two-year war and have been held without charge.
Also among those released were 250 Palestinians sentenced to prison terms, most of them convicted for deadly attacks on Israelis dating back decades, according to Israel's justice ministry.
