Southern Command said a navy vessel patrolling five miles off the Gaza coast stopped to inspect several Palestinian fishing craft.
When one of the fishing boats ignored orders to halt and sped toward the Khan Yunis coast, the patrol boat fired warning shots; when the fishing boat continued to flee, shots were fired at the boat.
The IDF spokesman said the boat reached shore at Khan Yunis, where the wounded fishermen were treated by Palestinian medics.
Abu Ula said one fisherman was shot in the face and the bullet had exited through his cheek, and the other was shot twice near the heart.
He claimed the patrol boat fired approximately 50 bullets at the Palestinian fishing boat.