Lebanon's Army said Israeli gunboats entered Lebanese waters four times on Saturday near Naqoura in the south of the country.
On Sunday, the Lebanese Army Command — Orientation Directorate issued a statement saying the gunboats crossed into Lebanese territorial waters between 3pm and 6.09pm at distances of up to 481 metres across the boundary.
The alleged breaches are being investigated in co-ordination with the United Nations Interim Force in south Lebanon, read the statement, reported by Lebanon's National News Agency.
Israel refuted the claims, saying there had been no crossing into the area by its forces.
The disagreement came just days after both nations, technically at war, approved a US-mediated maritime border deal.
Once signed, the deal will open the door for offshore energy exploration and mark a diplomatic departure from decades of war and hostility.
Under the agreement, disputed waters would be cut along a line straddling the Qana natural gasfield.
Lebanon will carry out the gas production, but Israel will be compensated for gas from its side of the line.
Lebanon has for years accused Israel of violating its airspace with drones and jets planes engaged in reconnaissance activities.
Beirut had also formally complained over the years to the UN Security Council.