Witnesses said the gunfire caused the boat to sink, with no injuries reported.
An Israeli military spokeswoman said the vessel “deviated from the designated fishing area” and that naval forces fired warning shots at the boat’s engine after it failed to respond to calls to turn back.
After shots were fired, the boat returned to the designated fishing area and did not sink, she said.
Under Israel’s maritime blockade, Palestinians are forbidden from fishing more than three nautical miles from the coast.
During the Oslo accords, Israeli and Palestinian negotiators had agreed on 20 nautical miles of fishing access along Gaza’s coastline.
The Gaza-based Al-Mezan Center for Human Rights says Israel detained 40 fishermen, injured five others and seized nine boats in 2011.