Israeli medical authorities said forensic teams were preparing to examine the body, which Hamas transferred on Friday via the Red Cross, and confirm its identity.
The Palestinian militant group had agreed to hand over the bodies of Shiri Bibas and her two young sons Kfir and Ariel along with the remains of a fourth hostage on Thursday under the ceasefire that has halted fighting in Gaza since January.
Four bodies were delivered and the identities of the Bibas boys and the other hostage, Oded Lifshitz, were confirmed.
But Israeli specialists said the fourth body was that of an unidentified woman and not Shiri Bibas, who was kidnapped along with her sons and her husband, Yarden, during the Hamas attack on Israel on October 7, 2023.
Basem Naim, a member of the Hamas political bureau, said "unfortunate mistakes" could occur, especially as Israeli bombing had mixed the bodies of Israeli hostages and Palestinians, thousands of whom were still buried in the rubble.
"We confirm that it is not in our values or our interest to keep any bodies or not to abide by the covenants and agreements that we sign," he said in a statement.
The failure to hand over the correct body and the staged public handover of the four coffins on Thursday caused outrage in Israel and drew a threat of retaliation from Netanyahu.
"We will act with determination to bring Shiri home along with all our hostages - both living and dead - and ensure Hamas pays the full price for this cruel and evil violation of the agreement," he said in a video statement.
Hamas said in November 2023 that the children and their mother had been killed in an Israeli air strike. Ismail Al-Thawabta, director of the Hamas-run Gaza government media office, said Netanyahu "bears full responsibility for killing her and her children".
But the Israeli military said intelligence assessments and forensic analysis of the bodies of the Bibas children indicated that they were deliberately killed by their captors. Chief military spokesperson Daniel Hagari said the boys were killed by the militants "with their bare hands", but gave no details.
The United Nations Human Rights Office said it had no information of its own on the hostage deaths and called for an effective investigation into the causes.
"The return of the remains of the deceased is a basic humanitarian goal," the office said.
The incident underscored the fragility of the ceasefire agreement reached with US backing and with the help of Qatari and Egyptian mediators last month.
Six living hostages were due for release on Saturday in exchange for 602 Palestinian prisoners and detainees, according to Hamas, and the start of negotiations for a second phase of the ceasefire was expected in the coming days.
Netanyahu's office confirmed it had been officially informed of the names of the six hostages to be released, which Hamas sources said was expected about 8.30am.
As the tension over the Gaza ceasefire rose, Netanyahu ordered the Israeli military to intensify operations in another Palestinian territory, the occupied West Bank, after a number of explosions blew up buses standing empty in their depots near Tel Aviv.
No casualties were reported but the explosions were a reminder of the campaign of suicide attacks on public transport that killed hundreds of Israeli civilians during the Second Intifada in the early 2000s.
Both Israel and Hamas have repeatedly accused the other of ceasefire violations, with Hamas threatening to delay the release of hostages over what it said was Israel's refusal to allow housing materials and other aid into Gaza, a charge Israel denied.
Despite the outrage over Shiri Bibas, there was no indication that Israel would not take part in talks over a second phase of the ceasefire deal.
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