It was not immediately clear whether the four had been arrested, the officials added.
The occupation military confirmed that naval fire had destroyed one boat it claimed 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 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.
"The forces followed the boat and identified it heading back towards Gaza, fully loaded," it said.
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.