The vessels will pass through Cyprus so as not to violate UN Security Council Resolution 1701.
The minister added that one of the vessels would undergo a technical checkup before it sails from Tripoli and that the Lebanese government was responsible for the decision.
Diplomatic sources in the United Nations said over the weekend that the UNIFIL headquarters in New York had warned Lebanon that UN naval forces would not allow any violation of Resolution 1701 and would prevent any such violation.
UN Resolution 1701, which ended the Second Lebanon War, stipulates that the United Nations Interim Force in Lebanon's role is to ensure that the region will not be used for any aggressive actions.
On Friday, Israel warned the UN that the security situation in the Middle East may be undermined as result of the Lebanese flotilla planning to head to the Gaza Strip.
In a letter relayed to UN Secretary-General Ban Ki-moon, Israel's Ambassador to the UN Gabriela Shalev said the "provocative" sail may affect security in the entire region.
Two ships are expected to leave from Lebanon to Gaza: Naji al-Ali – which will be carrying 25 European activists, including parliament members, and some 50 journalists – and Maryam – which is said to carry female activists with chemotherapeutic medications for women and children and humanitarian aid. It is unclear when the vessels will set sail.