Ibrahim al-Shawas, 36, died on Saturday after being shot in the head near Khan Yunus on Friday, they said. Witnesses said he was approaching a border fence near the town when a shot rang out from the Israeli side.
Aljazeera reported that al-Shawas was on his way to his farm when he was shot and killed.
His death brings the number of people killed since the start of the Palestinian intifada or uprising in September 2000 to 4721, including 3666 Palestinians and 981 Israelis.
Al-Shawas' death comes as Palestinian security forces widened their control in the Gaza Strip on Friday under orders from President Mahmud Abbas to prevent attacks on Israelis in another important move towards reviving peace talks.