Lebanese protested against Israeli attack with Turkish flags in Beirut and Palestinian refugee camps across the country also witnessed several demonstrations during which protesters chanted anti-Israeli slogans and raised Palestinian flags.
Israeli commandos stormed the ships before dawn and at least 19 activists on board were killed, most of them reportedly Turkish nationals.
"We hope they come back safely. My father is on the ship and he is injured but our blood is not more precious than the blood of all martyred Palestinians," said Adham Suleiman, the son of Lebanese activist Hani Suleiman, in Beirut.
Lebanese Parliament Speaker Nabih Berri also asked the foreign ministry to request a special session of the UN Security Council in order to discuss the attack.
Berri had contacted Foreign Minister Ali Shami and urged him to take action and ask the council to convene immediately, since Lebanon was currently its head, the country's state run National News Agency reported.
Earlier, Lebanon's Prime Minister Saad Hariri said the Israeli attack on the Gaza flotilla was "dangerous" and a "crazy move," which would inflame the region.
The premier called on the international community to take action and said Lebanon was in contact with a number of countries to coordinate responses to the incident.
Reports in Beirut said the head of the Lebanese mission to the "Freedom Flotilla" Hani Suleiman, had been wounded in the attack.
Lebanon's Hezbollah said on Monday Israel's attack against Gaza-bound aid ships in which at least 19 people were killed, was a "terrorist act that deserves international punishment".
"Israel's kidnapping of civilian hostages from international waters and their arrest constitutes a barbaric aggression and Israel bears complete responsibility if anything happens to them," Hezbollah lawmaker Hassan Fadlallah told Reuters.
"Any delay by the Security Council in moving quickly against this Israeli crime constitutes a cover-up. This never would have happened without international and U.S. silence over the Gaza blockade and the crimes that Israel commits against civilians."