The Lebanese army said on Tuesday that an Israeli gunboat had violated Lebanese territorial waters on Monday morning, an allegation denied by Israel.
This is the second such dispute this week as the countries work toward a maritime border demarcation.
On Sunday, Lebanon said in a statement that there were four violations where gunboats entered several hundred meters inside Lebanese waters and that authorities were discussing the violations with a United Nations Interim Force.
The alleged naval incursion took place in an area of the Mediterranean sea opposite Ras Naqura, on the border with Israel, the Lebanese army said.
In response, an Israeli military spokesperson said "there was no crossing" into Lebanese territorial waters on Monday.
The countries are technically at war but this month clinched a U.S.-brokered agreement to demarcate a maritime border. The deal awaits formal announcement by Washington.
Lebanon and Israel signaled their approval of the deal which laid out their respective maritime rights.
If finalized, the agreement - hailed by all three parties involved as a historic achievement - would mark a diplomatic departure from decades of war and hostility as well as opening the door to offshore energy exploration. But it is not likely to be finalized before the elections in Israel scheduled for November 1.