The ministry said an "Israeli enemy drone strike" killed one person in the town of Khiam, while another raid hit a motorbike and killed another person in Yohmor al-Shaqeef, elsewhere in south Lebanon.
The state-run National News Agency said the raid in Khiam killed a man who was repairing plumbing on the roof of a house.
The Israeli military said it killed a member of Hezbollah's elite Radwan force "who was involved in efforts to reestablish Hezbollah's terrorist infrastructure sites" in the Khiam area, and another in Yohmor who was involved in similar activities.
Israel has repeatedly bombed Lebanon despite a November ceasefire that sought to end over a year of hostilities with Hezbollah.
Under the truce, the militant group was to withdraw its fighters north of the Litani river, about 30 kilometres (20 miles) from the Israeli border, leaving Lebanon's army and United Nations peacekeepers as the only armed parties in the region.
Israel was to withdraw its troops from Lebanon but has kept them in five areas it deems strategic, reports UNB.