"At least five aircraft overflew the Bint Jbeil region (south of Beirut) and headed for the port town of Tyre" farther north, the official told AFP.
The security official said an Israeli MK-type reconnaissance aircraft flew over the south all night until dawn broke.
Tension remains high in the region two years after the 34-day summer war in 2006 between Israel and Lebanon's Shiite Hezbollah movement which devastated the south of the country.
Hezbollah chief Hassan Nasrallah, who is expected to speak later on Sunday about the deadly Israeli air attacks on Gaza, has threatened to "destroy" Israel if a new conflict erupts.
Israel says Hezbollah has "tripled its firepower" since the 2006 conflict and has pledged to attack Lebanese civilian locations in the event of renewed hostilities.
Israeli flights over Lebanon are in breach of UN Security Council resolution 1710, which in August 2006 ended the Israel-Hezbollah war.