The Palestinian Resistance Committees, an armed group in Gaza, said that it had fired the mortars.
The raids on Saturday came a day after Israel bombed tunnels, saying they were used to smuggle weapons into Gaza, a coastal territory under the de facto control of Hamas, an armed Palestinian political group.
The latest round of Israeli air raids are the first to target Palestinian tunnels in nearly two months.
Missile fire by Palestinian rocket squads has fallen since Egypt began efforts to ensure that a January 18 truce that ended Israel's 22-day offensive on Gaza holds.
Israel launched its war on Gaza with the stated aim of preventing armed groups in Gaza from firing rockets towards its territory.
At least 1,417 Palestinians were killed during the war, of whom 926 were civilians, a Palestinian human rights organisation says.
The Israeli military says the death toll was 1,166, of whom 295 were civilians. At least 13 Israelis, including three civilians, died over the course of the conflict.