Eight of the victims, four of them children, were killed in a strike on the village of Chimstar and five people died in an attack on the village of Bodai, the ministry said.
Both villages are in the Baalbek district.
In Beirut, an eight-storey building was struck with four missiles, including bunker-penetrating types designed to hit underground targets, a Lebanese security source said.
Israel has used bunker-busting weapons to kill senior Hezbollah figures, including its veteran leader Hassan Nasrallah in a strike on southern Beirut in September.
At the site of the Israeli strike in central Beirut, Hezbollah MP Amin Chirri said there had been no Hezbollah leader in the building that was struck.
The Israeli military made no immediate comment.
Saturday's blasts shook the capital about 4am and left a deep crater.
Beirut smelled strongly of explosives for hours afterwards.
Israel says it is targeting Hezbollah members in Lebanon and tries to avoid the deaths of civilians. (AP PHOTO)
Rescuers searched through rubble, in an area of the city known for its antique shops.
It was the fourth Israeli air strike this week targeting a central area of Beirut, in contrast to the bulk of Israel's attacks on the capital region which have hit the Hezbollah-controlled southern suburbs.
On Sunday an Israeli air strike killed a Hezbollah media official in the Ras al-Nabaa district of central Beirut.
The Israeli air force also struck Hezbollah targets in the southern suburbs of Beirut, the group's stronghold, the Israeli military said.
In a statement on actions on Saturday, it did not mention the strike on central Beirut.
It accused Hezbollah of embedding its infrastructure in civilian areas and using the population as human shields, allegations the group denies.
A man whose family was hurt in the strike in central Beirut tried to comfort a traumatised woman outside a hospital.
Car windows were shattered.
"There was dust and wrecked houses, people running and screaming, they were running, my wife is in hospital, my daughter is in hospital, my aunt is in the hospital," said the man, Nemir Zakariya, who held up a picture of his daughter.
"This is the little one, and my son also got hurt - this is my daughter, she is in the American University (of Beirut Medical Centre), this is what happened."
Separately, at least five people were killed and two wounded in an Israeli strike on Roum village in southern Lebanon on Saturday, according to the Lebanese state news agency.
Israel launched a major offensive against Hezbollah in Lebanon in September, following nearly a year of cross-border hostilities ignited by the war in the Gaza Strip, pounding wide areas of Lebanon with air strikes and sending troops into the south.
Israeli strikes killed at least 62 people and injured 111 in Lebanon on Thursday, bringing the toll since October 2023 to 3645 dead and 15,355 injured, Lebanon's health ministry said.
The figures do not distinguish between combatants and civilians.
Hezbollah and the Lebanese government accuse Israel of indiscriminate bombing that kills civilians.
Israel denies the allegation and says it takes numerous steps to avoid the deaths of civilians and it accuses Hezbollah of using human shields.
Hezbollah denies the accusation.
Hezbollah strikes in the same period have killed more than 100 people in northern Israel and the Israeli-occupied Golan Heights.
They include more than 70 soldiers killed in strikes in northern Israel and the Golan Heights and in combat in southern Lebanon, according to Israel.
The conflict began when Hezbollah, Iran's most important ally in the region, opened fire in solidarity with its Palestinian ally Hamas after it launched the October 7, 2023 attack on southern Israel.
