There was no immediate comment from Hamas.
This is the first fatality from internal fighting since a fragile truce between the rival factions was put in place.
"Hamas is trying to draw us [Israel] into their civil war"
Zafon, Beersheva, Israel
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More than 50 Palestinians died in the last round of fighting that started mid-May.
There have been sporadic clashes and continued tit-for-tat kidnappings, but the incidents were quickly resolved, as the two factions held talks in Cairo to cement their ceasefire. The talks ended on Wednesday.
Late on Wednesday, a brief gun battle broke out between gunmen from the two factions after security officials said they discovered a tunnel which they believed was to be used in an attack against Mahmoud Abbas, the Palestinian president.
There were no reports of injuries. The tunnel was six metres deep and ran around 23 metres from Gaza's main road to a Palestinian checkpoint close to the northern Erez crossing, used by foreigners and high-profile Palestinians to enter the Strip.