Eytan Buchman said the Air Force made "a successful hit" Thursday on what was described as a "terrorist site" between Beirut and Sidon, The New York Times reported.
Ramez Mustafa, a Lebanon-based official with the Popular Front for the Liberation of Palestine, said there were no casualties from the airstrike on Naameh, 19 miles south of Beirut.
In a statement, the Lebanese Army said an Israeli fighter jet fired one missile that struck a compound with tunnels used by the militant group.
"The [Israeli military] holds the Lebanese government accountable for yesterday's attack," Buchman said. "The [Israeli military] will continue to operate to safeguard the state of Israel and its citizens."
The Israel-Lebanon border has been mainly calm since 2006, the Times said.
The Israeli military said its Iron Dome missile defense system intercepted one rocket between the Israeli towns of Acre and Nahariya and two fell between buildings in Israeli villages, damaging property but causing no injuries. Another rocket appeared to have fallen in an open area.
"We see this as an unprovoked attack on the Israeli home front," Buchman said.
The Lebanese Army said in a statement an "unknown group" fired the Katyusha rockets from somewhere south of Tyre. The statement said an army unit found four wooden launching pads during a search of the area and that the army was searching for the perpetrators.
Israeli military spokesman Yoav Mordechai said on Army Radio Israel believed the matter was a "one-time event," given the location from which the rockets were fired.