As part of the agreement, Israel was supposed to release the prisoners last weekend after Hamas freed hostages from its Oct. 7, 2023, attack.
The incident raised new doubts about the future of the fragile ceasefire deal, which has paused over 15 months of war.
The remains were presumed to be of Shiri Bibas and her two children, Ariel and Kfir, as well as Oded Lifshitz, who was 83 when he was abducted.
The six to be released on Saturday are the last living hostages to be freed under the first phase of the ceasefire in Gaza.
The sides have carried out five swaps since the ceasefire went into effect last month, freeing 21 hostages and over 730 prisoners.
Hamas released seven of the hostages in front of the destroyed home of its slain leader, Yahya Sinwar, as thousands pressed in.
Israel overnight said it had received a list of information on the status of the hostages from Hamas.
The Hamas militant group has published the names of four hostages it says it will release on Saturday as part of the ceasefire in the Gaza Strip.
Israel believes a third of the remaining hostages are dead.
Israeli forces in Gaza killed Hamas’ top leader Yahya Sinwar, a chief architect of last year's attack on Israel that sparked the war.