The attack targeted a training ground used by Hamas's armed wing, the Ezzedine al-Qassam Brigades, which lies just east of Gaza City, they said.
The dead man was named by medics as Mahmud al-Hiqi, 27, and the other two, who were moderately injured in the strike, were also identified as Hamas militants.
The Israeli army had no immediate comment on the strike which hit an area where three Palestinians had been injured by Israeli tank fire earlier Thursday.
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