During a troop visit on Tuesday, Netanyahu referred to all above-ground and underground facilities that the militia had used for attacks on Israel, such as tunnels.
"This is the directive: leave nothing behind, and you are doing that," Netanyahu said according to the government press office.
In addition, soldiers should act immediately if they identified a threat to their lives, Netanyahu said.
He also ruled out a withdrawal of the army from the border area until Hezbollah was fully disarmed and no longer posed a threat to Israel.
Netanyahu described Hezbollah as the most important link in an axis of Iran's allies.
About eight per cent remain of what was once 150,000 rockets and projectiles, he said.
Israel had killed around 9000 "terrorists" in Lebanon, he said.
The most important measure had been to create buffer and security zones between Hezbollah and northern Israel.
The Lebanese government and Hezbollah describe the "security zone" unilaterally ordered by Israel as an occupation in breach of international law.
According to geographical calculations by Lebanese media, the area controlled by Israel in southern Lebanon covers around 620sq/km - about six per cent of the country's area.
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