The dead included two women and a Lebanese army soldier, the Health Ministry said in a statement on Sunday.
People were reported wounded in more than a dozen villages in the border area.
Demonstrators, some of them carrying Hezbollah flags, attempted to enter several villages to protest Israel's failure to withdraw from southern Lebanon by the 60-day deadline stipulated in a ceasefire agreement that halted the Israel-Hezbollah war in late November.
Israel has said that it needs to stay longer because the Lebanese army has not deployed to all areas of southern Lebanon to ensure that Hezbollah does not re-establish its presence in the area.
The Lebanese army has said it cannot deploy until Israeli forces withdraw.
The United Nations is urging Israel and Lebanon to comply with the ceasefire agreement. (AP PHOTO)
The Israeli army blamed Hezbollah for stirring up Sunday's protests.
It said in a statement that its troops fired warning shots to "remove threats in a number of areas where suspects were identified approaching."
It added that a number of suspects in proximity to Israeli troops were apprehended and were being questioned.
Lebanese President Joseph Aoun said in a statement addressing the people of southern Lebanon on Sunday that: "Lebanon's sovereignty and territorial integrity are non-negotiable, and I am following up on this issue at the highest levels to ensure your rights and dignity".
He urged them to "exercise self-restraint and trust in the Lebanese Armed Forces."
The Lebanese army, in a separate statement, said it was escorting civilians into some towns in the border area and called on residents to follow military instructions to ensure their safety.
Parliament Speaker Nabih Berri, whose Amal Movement party is allied with Hezbollah and who served as an interlocutor between the militant group and the US during ceasefire negotiations, said that Sunday's bloodshed: "is a clear and urgent call for the international community to act immediately and compel Israel to withdraw from occupied Lebanese territories".
An Arabic-language spokesperson for the Israeli military, Avichay Adraee, posted on X that Hezbollah had sent "rioters" and is "trying to heat up the situation to cover up its situation and status in Lebanon and the Arab world".
He called on Sunday morning for residents of the border area not to attempt to return to their villages.
UN Special Coordinator for Lebanon Jeanine Hennis-Plasschaert and the head of mission of the UN peacekeeping force known as UNIFIL, Lieutenant General Aroldo Lázaro, called in a joint statement for both Israel and Lebanon to comply with their obligations under the ceasefire agreement.
"The fact is that the timelines envisaged in the November understanding have not been met," the statement said.
"As seen tragically this morning, conditions are not yet in place for the safe return of citizens to their villages along the Blue Line."
Recommitment urgently needed… — Jeanine Hennis (@JeanineHennis) pic.twitter.com/1bDXq12n0MJanuary 26, 2025
An AP team was stranded overnight at a UNIFIL base near Mays al-Jabal after the Israeli army erected roadblocks on Saturday while they were joining a patrol by peacekeepers.
The journalists reported hearing gunshots and booming sounds on Sunday morning from the base, and peacekeepers said that dozens of protesters had gathered nearby.
In the village of Aita al Shaab, families wandered over flattened concrete structures looking for remnants of the homes they left behind.
No Israeli forces were present.
"These are our houses," said Hussein Bajouk, one of the returning residents.
"However much they destroy, we will rebuild."
On the other side of the border in the kibbutz of Manara, Orna Weinberg surveyed the devastation of the recent conflict on her neighbours and the Lebanese villages on the other side of the frontier.
The sound of gunfire sporadically popped in the distance.
"Unfortunately, we have no way of defending our own children without harming their children," Weinberg, 58, said.
"It's a tragedy to all sides."
Some 112,000 Lebanese remain displaced, out of over 1 million who fled their homes during the war.
