It said five missiles and eight shells were fired from the southern section of the Gaza Strip and the northern part of the Palestinian enclave, respectively.
No casualties have been reported.
Responsibility for the attack was claimed by the armed wing of the ruling Hamas movement, Izeddin al Qassam Brigades, which said they had fired 74 mortar shells and 19 missiles "in retaliation for Zionist crimes against our people."
Hamas and al-Aqsa Martyrs Brigades (Fatah) militants rallied in the Gaza Strip Monday vowing to avenge nine fellow activists killed over the weekend by Israeli forces.
"The Palestinian people have a right to resist the occupation," a Hamas leader said at the meeting.
The Israeli security service, Shabak, said underground tunnels had been detected that could be used by terrorists to infiltrate Israeli territory, abduct soldiers and plant bombs in cities, including Tel Aviv.
The latest military action in the area was sparked by the abduction of an Israeli corporal, Gilad Shalit, in June. As three Palestinian militant groups claimed responsibility for the incident, Israel sent troops into Gaza to secure the corporal's release.
