President Emile Lahoud denounced the raid as "another violation of Lebanese sovereignty and part of the hostile Israeli practices against Lebanon", an official statement said on Tuesday.
Lahoud also "asked the concerned authorities to lodge a letter of complaint with the United Nations Security Council over the new Israeli aggression".
Officials said Foreign Minister Jean Obeid had instructed Lebanon's ambassador to the United Nations, Sami Kronfol, to send such a letter, complaining of the "new aggression".
The letter of complaint was submitted to the Security Council on Tuesday.
Beirut also "reserved the right for Lebanon to request a council meeting if and when it sees fit", one official said.
Israel said the attack was a warning to Lebanon and patron Syria against cross-border attacks.
As Israeli officials warned of dire consequences if Lebanon was used as a "springboard" for further attacks by pro-Syrian groups.
On Monday night, Israeli jets bombed suspected positions of the Popular Front for the Liberation of Palestine-General Command in Naameh, 20km south of the Lebanese capital.
The attack, which the PFLP-GC said had inflicted no casualties, was in response to an attack earlier on Monday that Israel said targeted one of its naval vessels patrolling in Israeli territorial waters.
"The savage and hostile raid did not inflict casualties, but left material damage"
The raid on Naameh was the first air strike so close to the capital since the Israeli troop pullout from southern Lebanon in May 2000 after 22 years of occupation.
A spokesman for the UN Interim Forces in Lebanon said an investigation was started after three missiles were fired on Monday from an area near the peacekeeping forces' headquarters in the border town of Naqura.
A PFLP-GC official said late on Monday the warplanes had fired two missiles at disused positions of the group.
It later explained in a statement that "as part of a state terrorism programme practised by the Zionist entity ... enemy warplanes raided a PFLP-GC medical centre in Naameh, which provides medical and social services to the people".
"The savage and hostile raid did not inflict casualties, but left material damage," it said.