Palestinian medics search the rubble following Israeli strikes in Gaza City. AFP
Citing documents found during its forces' Gaza offensive, the military said Mahmud Bassal was "an active terrorist" in the Islamist Palestinian militant group.
It issued copies of what it said were Hamas membership lists to the media, without clarifying where or how the undated documents were obtained.
The Israeli military accused Bassal of serving Hamas's objectives by spreading false and unverified information about its operations in Gaza.
"This is a false accusation," Bassal told AFP. "I do not work for any military organisation," he said, adding that the agency's mission was guided by international law.
The civil defence agency has operated in the Gaza Strip for decades, deploying rescuers to rush victims of Israeli air strikes to the hospital.
The organisation is often cited by international media outlets.
With access restricted and conditions on the ground chaotic, it remains nearly impossible to independently verify casualty figures or the circumstances of deaths reported by the agency.
The army's accusation comes as it faces criticism from the civil defence, which alleges Israeli forces recently killed civilians near food distribution centres.
The Israeli war on Gaza began on October 7, 2023, and has killed 54,772, the majority civilians. The UN considers these figures reliable.
Short link: