Netanyahu's authorisation of direct talks with Lebanon came amid disagreement over whether the Middle East ceasefire deal included a pause in fighting between Israel and Hezbollah, and a day after Israel pounded Beirut with airstrikes that killed more than 300 people.
He later stressed there was no ceasefire between Israel and Lebanon.
There was no immediate response from Lebanon. But Israel-Lebanon negotiations were expected to begin next week at the State Department in Washington, according to sources.
The prospect of talks appeared to bolster the tentative ceasefire in the Iran war that has staggered under the weight of Israel's bombardment of Beirut, Tehran's continued chokehold on the Strait of Hormuz and uncertainty over whether talks can find common ground.
However later Thursday, US President Donald Trump appeared to cast doubt on the effectiveness of the ceasefire, writing on his social media platform: "Iran is doing a very poor job, dishonourable some would say, of allowing Oil to go through the Strait of Hormuz."
"That is not the agreement we have!" Trump wrote.
After declaring victory with the ceasefire announcement, both Iran and the US appeared to apply pressure on each other. Semiofficial news agencies in Iran suggested forces have mined the Strait of Hormuz, a crucial waterway for oil that Tehran has closed. Trump warned that US forces would hit Iran harder than before if it did not fulfill the agreement.
Questions also remained over what will happen to Iran's stockpile of enriched uranium at the heart of tensions, how and when normal traffic will resume through the strait, and what happens to Iran's ability to launch future missile attacks and support armed proxies in the region.
Iranian President Masoud Pezeshkian said in a message on Telegram that Iran's decision to accept a ceasefire was made unanimously by senior government leaders and approved by the supreme leader. He said the ceasefire "is not a sign of weakness but a way to solidify Iran's proud victories."
Trump said Thursday that he has asked Netanyahu to dial back the strikes in Lebanon.
Netanyahu, whose government rebuffed a historic offer for direct talks with Lebanon last month, said in a statement that he had given instructions to start peace talks as soon as possible, which would also include disarming Iran-aligned militant group Hezbollah.
"In light of Lebanon's repeated requests to open direct negotiations with Israel, I instructed the cabinet yesterday to start direct negotiations with Lebanon as soon as possible," he said.
"The negotiations will focus on disarming Hezbollah and establishing peaceful relations between Israel and Lebanon."
Israel said Thursday it killed an aide to Hezbollah leader Naim Kassem, Ali Yusuf Harshi. Hezbollah did not immediately respond to a request for comment.
Semiofficial news agencies in Iran published a chart Thursday suggesting the country's paramilitary Revolutionary Guard put sea mines into the Strait of Hormuz during the war — a message that may be intended to pressure the United States.
The chart, released by the ISNA news agency and Tasnim, showed a large circle marked "danger zone" in Farsi over the route ships take through the strait, through which 20 per cent of all traded oil and natural gas once passed.
Only a trickle of ships have transited since the war began after several were attacked, and Iran threatened to hit any that it deemed connected to the US or Israel. Ships appeared to continue to avoid the strait even after the ceasefire.
The head of the United Arab Emirates' major oil company, Sultan al-Jaber, said some 230 ships loaded with oil were waiting to get through the strait and must be allowed "to navigate this corridor without condition."
with DPA