The bodies will be taken to Israel's National Centre of Forensic Medicine for identification.
Earlier, Hamas said it had recovered the bodies of hostages Amiram Cooper and Sahar Baruch.
On Tuesday, Israeli Prime Minister Benjamin Netanyahu ordered strikes on Hamas that left more than 100 people dead, including dozens of children.
President Donald Trump said on Wednesday on Air Force One that "nothing's going to jeopardize" the Gaza cease-fire. He said he would "take out Hamas very easily."
An attack on the Israel Defense Forces and the return of remains from a hostage already returned in 2023 were the purported reason for the attack from Israel.
The death of IDF reservist Yona Efraim Feldbaum, 37, is the reason for the attack on Hamas, said Israeli Defense Minister Israel Katz. He called it another beach of the cease-fire.
Feldbaum was killed by gunfire while his team was destroying an underground tunnel in Rafah.
Hamas denied having anything to do with the attack in Rafah. It said it was fully committed to the cease-fire but was postponing the return of remains of another hostage recovered on Tuesday because of the attack by Israel.
The IDF released a video that it said shows Hamas staging the recovery of hostage remains then passing them along to the Red Cross.
"It is unacceptable that a fake recovery was staged, when so much depends on this agreement being upheld and when so many families are still anxiously awaiting news of their loved ones," the Red Cross said in a statement.
There are still 13 dead hostages in Gaza, and 11 of them are Israeli. One is from Tanzania and the other is Thai.
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