Israeli army spokesman Avichay Adraee said Rasmi Abu Malhous was killed in a raid in the Gaza Strip's Deir al-Balah before a ceasefire took hold on Thursday morning.
Adraee alleged on Twitter he was a commander of a rocket unit.
The Gaza health ministry earlier said eight members of the Abu Malhous family, including five children, were killed in an Israeli strike on their family home.
Residents and relatives disputed that he was affiliated with Islamic Jihad, saying he had been a military police officer for the Palestinian Authority.
Israeli military spokesman Jonathan Conricus told AFP: "He was an Islamic Jihad commander and he, like many others, have the tactic of hiding ammunition and military infrastructure in their own residence.
"Of course we try always to minimise the amount of non-combatants killed or injured," he added.
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