An Israeli military spokesman confirmed the raids, saying a small number of soldiers were searching for tunnels and mines, describing it as “restricted, pinpoint attacks.”
No more details were provided and no indication given as to whether the action would be expanded into a larger operation.
Israel hasn't ruled out the possibility of a major land offensive and has sent its troops over the border several times in recent days, returning soon afterwards.
Israeli forces also re-entered the central Gaza Strip in the latest incursion in a three-week military push in the Palestinian territory.
Three Palestinians were reported to have been killed - including a member of the armed wing of - and 20 others injured by a missile fired from a pilotless drone.
The Israeli army said five of its soldiers were injured in heavy fighting near the Maghazi refugee camp in the Gaza Strip.
Death toll rises
Twenty-one civilians were reported to have been killed and 30 others wounded in Israeli air attacks in southern Lebanon early Wednesday morning.
The biggest toll was in the village of Srifa near the southern port city of Tyre, where 10 houses were destroyed.
Israeli gunboats were reported to have also took part in the attack on the village, which is about 30 kilometres northeast of Tyre.
"At least 10 houses were destroyed. There are tens of people dead, we don't know how many," a villager told the AFP news agency.
In Salaa, another village near Tyre, 10 members of a family were buried in the rubble when their home was completely destroyed during another Israeli air raid.
"The raid by an Israeli fighter-bomber completely destroyed the two-storey house which collapsed on to its occupants, a family of 10, who are almost certainly dead," a Lebanese police officer said.
Another six people were killed, including a Lebanese woman and her three children, a Sri Lankan and a Sudanese national, were killed in air bombardment on the town of Nabatiyeh, northeast of Tyre, police said.
Five more civilians were killed in an air raid against a number of trucks near in eastern Lebanon, police said.
More than 260 people have been killed and 500,000 made homeless in the seven days of fighting,
The number wounded in Lebanon since hostilities broke out on July 12 now stands at more than 500, according to an AFP tally based on official figures.
The vast majority of the dead so far have been civilians with the remainder being 23 soldiers and six fighters of Shiite militant group Hezbollah.
Israel's count is 25 dead - 13 civilians in Hezbollah rocket attacks, and 12 servicemen.
Infrastructure destroyed
Damage to Lebanon's civilian infrastructure has been extensive with craters punched into the tarmac of Beirut's airport, making it unusable. Military airports have also been put out of action.
Roads have been bombed, including the main exit route for foreigners trying to flee.
The highway from Beirut to the Syrian capital Damascus was cut on Tuesday after being repeatedly hit in recent days.
At least 38 other roads around Lebanon have also been cut, including several linking Beirut to its southern suburbs, a Hezbollah stronghold.
About 45 bridges have been destroyed or badly damaged, including three major ones.
Ports have been hit, including the two biggest, in Beirut and the northern city of Tripoli.
Around 15 petrol stations have been blown up, along with fuel depots and water pumping stations.
At least 100 residential buildings have been destroyed in southern Lebanon, and entire blocks in Beirut's southern suburbs, home to 500,000 people, have been levelled.
The headquarters of Hezbollah, a 12-building complex, has been the target of especially intensive bombing that has left nothing standing.