The fishermen were transferred to Ash-Shifa hospital for treatment of moderate injuries, medical official Adham Abu Silmiya said.
An Israeli military spokeswoman said the army had no record of such an event.
Fishermen in Gaza are calling for protection after four years of siege.
At a sit-in Thursday in Gaza's port, a group of fishermen rejected Israel's blockade policy, which for four years has limited their ships to the near coast at risk of being fired upon.
The sea off Gaza has been mostly off limits since June 2006 when Israel imposed a tight blockade on the territory after militants there snatched Israeli soldier Gilad Shalit, who is still being held.
The blockade was tightened a year later when the Islamist Hamas movement seized control of the territory, ousting forces loyal to the Western-backed Palestinian Authority.
Israel took steps to ease the measure last summer following a wave of international pressure after its troops staged a botched raid on an aid flotilla which was trying to break the embargo, killing nine Turkish activists.
On Thursday, fishermen appealed to the UN and human rights organizations to end the naval siege and pressure Israel to increase the area of fishing as well as "bring Israel into account for its crimes."
Mohammad Al-Hisi, one of the fishermen, told Ma'an that "the occupation's forces destroyed my small boat, which I depend on for my livelihood. And no one cares. I just want my livelihood."
The fishermen say they want international protection against Israeli attacks at sea.
Mustafa Al-Jarbu, another protester, explained that the sit-in was in protest of the "vicious acts" carried out by the Israeli army against fishermen, which have injured hundreds and killed dozens.
Three Gaza fishermen wounded after their boat was attacked off Khan Younis
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KHAN YOUNIS, (PIC)-- The crew of a fishing boat survived an attack by the Israeli occupation navy which took place late Thursday evening off the southern Gaza Strip Khan Younis shores, three of them were injured. Palestinian naval sources told PIC correspondent that an Israeli navy boat rammed the fishing boat carrying a crew of seven fishermen from behind resulting in the injury of 3 fishermen and extensive damage to the boat. The information office of the civil defence department said in a statement that sea rescue teams managed to rescue the crew and recover the damaged boat, adding that three of the crew suffered injuries varying from broken bones to bruises. Director of sea rescue, Captin Yahya al-Tayeh, said that the team faced difficulties towing the damaged boat to the fishermen’s wharf in Gaza City. Tayeh added that this was not the first time fishermen were targeted by the occupation navy which is trying to tighten the noose on the Gaza Strip.
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The three men were moved to Gaza City hospital for treatment; doctors said the three sustained moderate wounds. According to witnesses report, the Israeli navy boat attacked the fishermen boat and rammed it injuring the three men and though them to sea. 
