The 32-year-old died in hospital in Gaza City after he and two other fishermen in the same boat were fired upon by the Israeli navy.
The two other fishermen were arrested and taken to Israel, spokesman Ashraf al-Qudra said.
A spokeswoman for the Israeli army was unable to confirm the shooting when contacted by AFP.
Under the terms of Israel's eight-year blockade of the Palestinian territory, Gaza's fishermen have the right to trawl the waters up to six nautical miles off the coast.
But fishermen have said the Israeli navy opens fire before they reach that limit.
Around 4,000 fishermen work in Gaza, more than half of whom live below the poverty line.
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