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.
An Israeli army spokeswoman told AFP that four Palestinian boats had strayed out of their designated fishing zone yesterday.
"Soldiers fired warning shots then targeted the engines of two of the boats, which were then transferred to Israel for investigation," she said. "The two other boats were able to return to Gaza."
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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.