Gaza medical official Adham Abu Salmiya said the man was taken to Shifa hospital in Gaza City with moderate injuries to his legs.
An Israeli army spokeswoman said the fishing boat "deviated from the designated fishing area and the navy called on it to stop, but when it did not respond they fired warning shots at the boat engine."
In early December, the Al-Mezan Center for Human Rights said Israel has detained 40 fishermen, injured five others and seized nine boats since the start of the year.
Under Israel's maritime blockade, Palestinian fishers are forbidden from fishing more than three nautical miles from the coast.
During the Oslo accords negotiators had agreed on 20 nautical miles of fishing access along Gaza's coastline.
Noting that most Gaza residents were dependent on food aid, the International Red Cross said in July that Gaza's fishing industry had almost disappeared due to Israeli restrictions.
In a separate incident Friday, Israeli artillery fire struck near the eastern cemetery in the Shjaiya neighborhood, onlookers said.
There were no reports of injury or damage in that incident.
Israeli Gunboats Open Fire at Palestinian Fishermen in Gaza; One Fisherman Injured
At approximately 11:00 am on Friday 16 December 2011, Israeli naval vessels patrolling the Gaza sea opened fire on a Palestinian fishing boat about 1.5 miles off the coast west of Gaza City, opposite the Ash-Shati’ refugee camp. The Israeli forces targeted Zaki Tarroush, 45, from Beit Lahiya, who sustained two bullet wounds in the right hand and leg. He was admitted to Shifa Hospital.