Israel recovered the bodies of six hostages from a tunnel in southern Gaza where they were apparently killed not long before Israeli troops reached them, the military said on Sunday.

"According to our initial estimation, they were brutally murdered by Hamas terrorists a short time before we reached them," military spokesperson Rear Admiral Daniel Hagari told reporters in a briefing.

The bodies of Carmel Gat, Hersh Goldberg-Polin, Eden Yerushalmi, Alexander Lobanov, Almog Sarusi and Ori Danino had been found underground in the city of Rafah and returned to Israel, he said.

"The heart of an entire nation is shattered to pieces," said President Isaac Herzog, whose post is largely ceremonial. "I embrace their families with all my heart, and apologize for failing to bring them home safely."

There was no immediate comment from Prime Minister Benjamin Netanyahu, who is under pressure at home and abroad to reach a ceasefire deal that includes the release of remaining hostages.

U.S. President Joe Biden, who has closely followed the fate of the hostages seized on Oct. 7, said the six included Israeli American Goldberg-Polin.

"I am devastated and outraged," Biden said in a statement issued by the White House.

Days earlier, hostage Qaid Farhan Alkadi, a member of the Bedouin community in southern Israel, was rescued about a kilometre away, Israel's Hagari said.

After Alkadi was located, troops were told to be cautious because other hostages might be in the area, but there had been no precise information on their location, he said.

The six recovered bodies were from about 250 hostages taken in Hamas' killing spree through southern Israel on Oct. 7 that sparked the war in Gaza. About 1,200 people were killed in the assault, according to Israeli tallies.

Since then, at least 40,691 Palestinians have been killed and 94,060 injured in Israel's military offensive in Gaza, the enclave's health ministry said in a statement on Saturday.