The handover followed Israel's return on Friday of the bodies of 30 Palestinians to Gaza.
That completed an exchange after militants earlier this week turned over remains of two hostages, a sign that the tense Israel-Hamas ceasefire agreement was edging forward.
The unidentified remains of the three people were returned late on Friday to Israel, where they were being examined overnight.
At the time, a military official warned that Israeli intelligence suggested they did not belong to any of the hostages taken by Palestinian militants during the October 7, 2023, attack on southern Israel that sparked the war.
The Israeli official spoke on condition of anonymity because they were not authorized to talk to the media.
Israeli Prime Minister Benjamin Netanyahu's office on Saturday confirmed that the remains did not belong to any of the hostages, without giving further details.
Hamas's armed wing said in a subsequent statement that it had offered to hand over samples on Friday of unidentified bodies, but Israel had refused to receive them and asked for the remains for examination.
"We handed the bodies over to stop the claims of Israel," the statement said.
It was unclear who the remains belonged to.
Since the US brokered ceasefire between Israel and Hamas took effect on October 10, Palestinian militants have released the remains of 17 hostages that were held in Gaza for the past two years.
But the process of returning the bodies of the last 11 remaining hostages, as called for under the truce deal, is progressing slowly, with militants releasing just one or two bodies every few days.
The total number of Palestinian bodies returned by Israel since the ceasefire began now stands at 225.
Only 75 of those have been identified by families, according to Gaza's health ministry.
It is unclear if those returned were killed in Israel during the October 7, 2023 attack, whether they died in Israeli custody as detainees or were recovered from Gaza by troops during the war.
The fragile truce faced its biggest challenge earlier this week when Israel carried out strikes across Gaza that killed more than 100 people, following the killing of an Israeli soldier in Rafah, Gaza's southernmost city, and the incomplete return of hostages.
