It came a day after Palestinian militants returned the remains of Israeli hostage Dror Or, who the Israeli military says was killed by the militants in their October 7, 2023, attack.
Israel has agreed to return 15 Palestinian bodies for each hostage returned.
With the latest swap, Israel has sent back to Gaza a total of 345 Palestinian bodies since the exchanges started in October, according to the Gaza health ministry.
Two hostages - one Israeli and one Thai national - remain in Gaza.
Hamas said it was determined to uphold its side of the agreement and return them both.
Turkish, Qatari and Egyptian officials met Wednesday in Cairo to discuss the second phase of the ceasefire, which began in October and has held despite accusations by both sides of violations.
The next phases of the agreement include deploying an international stabilisation force and developing an international body to govern Gaza and oversee reconstruction.
An armed international stabilisation force will be tasked with keeping security and ensuring the disarmament of Hamas, a key demand of Israel. Indonesian officials have said they plan to deploy 20,000 peacekeepers to the force.
Major questions hang over nearly every part of the plan and the time frame for implementation.
In the meantime, nearly all Palestinians remain displaced and dependent on humanitarian aid, Hamas retains significant control over nearly half of Gaza and the rebuilding of the territory has barely begun.
Gaza's health ministry said only 99 bodies out of the 345 Israel had returned had been identified.
They say identifying the remains is complicated by a lack of DNA testing kits in Gaza.
Meanwhile, Israel mourned the latest hostage to be returned by the Palestinian militants, Dror Or.
Israel's military said Or and his wife, Yonat Or, were killed by militants who overran their community of Kibbutz Beeri on October 7, 2023.
Before they were killed by the militants, the couple evacuated two of their children from their burning house through the window, the Hostages Families Forum said.
The decision ultimately saved the children's lives - Alma and Noam were abducted by the militants and released in a hostage deal in November 2023.
In total, Palestinian militants killed some 1200 people across southern Israel and abducted 251 to Gaza in their October 7, 2023, attack that kickstarted the war in Gaza.
With the return of Or's remains, almost all of the hostages or their remains are out of Gaza.
Hamas said the militant group was committed to handing over the remaining two hostages and wrapping up the exchange, but it called for mediators to pressure Israel to stop its "violations" of the ceasefire.
A Palestinian man was killed when Israeli troops opened fire on Wednesday on a group of people east of the Maghazi refugee camp in central Gaza, a hospital said.
They were the latest casualties among Palestinians since a ceasefire deal brought the war to a halt in Gaza in October.
Also on Wednesday, the military said its troops struck a group of six militants in the southern city of Rafah, killing one.
Since the ceasefire took effect on October 11, the Gaza health ministry said, 345 Palestinians were killed and 889 were wounded in the strip as of Tuesday.
It said at least 69,775 Palestinians had been killed and 170,863 injured in Israel's offensive in Gaza.
