It was not immediately clear whether the four had been arrested, the officials added.
The Israeli military confirmed that naval fire had destroyed one boat it said had been involved in smuggling, but had no information about the four fishermen reported missing.
The two wounded fishermen were pulled out of the water off the southern port of Rafah after the Israeli fire destroyed both boats, a Hamas security official said.
The Israeli military said that naval vessels had tracked a boat engaged in smuggling from nearby Egypt.
"The navy identified a fishing boat which had left the Gaza shore and went down towards Egypt," a statement said.
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"The forces followed the boat and identified it heading back towards Gaza, fully loaded," it said, adding that Israeli warships had fired warning shots before targeting the vessel when it failed to respond.
"The smuggling attempt was foiled and the target was destroyed," it said, without indicating what the boat had been carrying.
Under the terms of Israel's eight-year blockade of the Palestinian territory, Gaza's fishermen have the right to trawl the waters up to six nautical miles off the coast.
There are around 4,000 fishermen working in Gaza, more than half of whom live below the poverty line.
The waters off Rafah, a town that straddles the Gaza-Egypt border, have become an increasingly important smuggling route since Egyptian security forces destroyed a network of tunnels running under the land border.