The bodies of two men in their 20s who had each been shot in the head washed ashore and were collected by local medics, the head of Gaza emergency services, Muawiya Hassanein, said.
On Monday, Israel attacked a boat carrying what it said was "a squad of terrorists wearing diving suits on their way to execute a terror attack."
A survivor who was on shore at the time of the attack said the six men on the boat were members of the Al-Aqsa Martyrs' Brigades, an armed group which is loosely tied to the secular Fatah movement of Western-backed president Mahmud Abbas, but that there were no weapons on the boat.
He said they were doing swimming exercises some 100 metres (yards) off the coast when they were attacked by Israeli naval forces.
The incident came as Israel faced an international outcry over its bloody seizure of an aid flotilla bound for Gaza, in which nine Turkish activists -- one holding US citizenship -- were shot dead.
Israel and Egypt tightened already strict Gaza border closures when the Islamist Hamas movement seized power in June 2007, and Israel maintains a tight naval blockade on the impoverished territory of 1.5 million people.