It was not immediately clear how Youssef Ziyadne had been killed but Lieutenant Colonel Nadav Shoshani said his death did not appear to have been recent.
"We are currently investigating the circumstances of his death and we are also investigating the findings regarding his son," he told a briefing with reporters.
"These findings raise concern for his life and they are still being examined at this moment," he said, without giving details.
Earlier Defence Minister Israel Katz said in a statement that the bodies of both men had been recovered.
Yesterday, the IDF and ISA located and recovered the body of the hostage Youssef Ziyadne from an underground tunnel in the area of Rafah in Gaza, and returned his body to Israel.— Israel Defense Forces (@IDF) Youssef, 53, was the father of 19 children and lived in Rahat. Youssef was abducted on Oct. 7, 2023… pic.twitter.com/0WK6kl80KsJanuary 8, 2025
Shoshani said special forces soldiers had conducted a "complex and difficult operation" in a tunnel in the area of the southern Gaza city of Rafah on Tuesday, and that the body of Ziyadne had been recovered close to bodies of armed guards from Hamas or another Palestinian militant group.
Two other children of Ziyadne, who were also abducted at the same time, were released in an exchange of hostages for Palestinian prisoners that took place in November 2023.
The recovery of Ziyadne's body took place as negotiators continued talks in Doha to halt the fighting in the Gaza Strip and bring the remaining hostages back as part of a deal that would include the return of a number of Palestinian prisoners held by Israel.
Palestinian medical workers said on Wednesday an Israeli air strike killed at least 10 people in a multi-storey house in the Sheikh Radwan neighbourhood of Gaza City while another killed 10 in other parts of the city.
In Deir al-Balah city in central Gaza, where hundreds of thousands of displaced Palestinians are sheltering, and in Jabalia, the largest of Gaza's eight historical refugee camps, a total of seven people were killed, they said.
Israel's military said it struck Hamas militants operating in a school building in Jabalia and that it took steps to minimise risk to civilians.
Israel launched its assault on the enclave after Hamas fighters stormed across the border 15 months ago, killing 1200 people and taking more than 250 hostages, according to Israeli tallies.
More than 46,000 Palestinians have been killed in Israel's air and ground war against Hamas, according to health officials in the Gaza Strip.
