On Wednesday evening the Lebanese army said it had fired at two or three drones that were violating its airspace, before they all returned across the border.
The Israeli army said its aircraft returned undamaged.
The incident comes after the Iran-backed Lebanese movement Hezbollah accused Israel of carrying out a drone attack Sunday on its Beirut stronghold.
According to Hezbollah, the attack involved two drones, one of which exploded, causing some damage to the group’s media centre, but no injuries. Israel has not claimed responsibility for the incident.
The alleged attack came after Israel launched strikes in neighbouring Syria to prevent what it said was an impending Iranian drone attack on Israel.
Hezbollah chief Hassan Nasrallah said two Hezbollah fighters were killed in the strikes, and in a televised speech on Sunday warned of retaliation for the Beirut drone incident.
"From now on we will confront Israeli drones in Lebanon's sky and work to down them," he said.
President Michel Aoun said on Monday that Lebanon had a right to defend itself.
On Tuesday, Israeli Prime Minister Benjamin Netanyahu warned Lebanon, Nasrallah and the head of Iran's elite Quds Force to "be careful".
Though tensions are high between Israel and Hezbollah, who last fought a war in July 2006, the Lebanese movement said a full-out war was unlikely.
"I rule out that the atmosphere is one of war, it is one of a response to an attack," Hezbollah deputy leader Sheikh Naim Qassem said in a TV interview on Tuesday night. "Everything will be decided at its time."