A strike killed 11 people in the village of Mazrat Beit Salibi, according to a breakdown given by the ministry.
Another strike in the town of Bednayel, also in the Baalbek area, killed eight others, it added.
Earlier on Wednesday, the Israeli military struck Baalbek after calling for evacuations, witnesses said.
Baalbek is noted for its UNESCO-listed ancient Roman temple complex. (AP PHOTO)
"The whole city of Baalbek was shaking as loud sounds of explosions were heard," a witness told DPA.
Residents earlier fled the affected areas in panic as loudspeakers in mosques across Baalbek called on people to leave the city.
Around 80,000 people live in Baalbek, which is known for its Roman temples that have been designated a UNESCO World Heritage Site.
In addition, many internally displaced civilians have sought refuge in the area - considered a Hezbollah stronghold - since Israel launched its ground offensive in southern Lebanon in late September.
Also on Wednesday, the Lebanese news agency NNA said that Israeli troops were trying to enter the key town of Khiam.
A witness in the area told DPA that Israeli forces entered the town from the east. According to NNA, several Israeli tanks had already advanced to the eastern outskirts of Khiam on Tuesday.
The troops attempted to enter the city "under heavy fire cover from fighter jets, drones and artillery," NNA reported.
Separately, Israel pummelled the Gaza Strip with new bombardments that killed at least 20 people, Palestinian medics say, a day after one of the deadliest single strikes of the year-old war killed scores in the north of the enclave.
Israeli strikes on southern Lebanon continue with more than 2700 killed since hostilities escalated. (EPA PHOTO)
Eight of Wednesday's victims were killed in a strike on the Salateen area of Beit Lahiya in northern Gaza. The area is near where medics said at least 93 people were killed or missing on Tuesday in an Israeli strike Washington called "horrifying".
The Israeli military assault that has laid waste to the Gaza Strip and killed tens of thousands of people shows no signs of slowing as Israel wages a new war in Lebanon and its backer the United States tries after a year of failed attempts to broker ceasefires for both.
Northern Gaza, where Israel said in January it had dismantled militant group Hamas' command structure, is currently the focus of the military's assault. It sent tanks into Beit Lahiya and the neighbouring towns of Beit Hanoun and Jabalia earlier this month to flush out Hamas militants who it said had regrouped in the area.
The new operation has killed hundreds of Palestinians, medical workers say, and has helped choke aid and food supplies to their lowest level since the beginning of the war.
Officials in Beit Lahiya issued a statement urging world powers and aid agencies to halt Israel's attacks and bring in basic medical supplies, fuel and food, saying the latest military actions had left the area "without food, without water, without hospitals, without doctors."
Dr Eid Sabbah of Beit Lahiya's Kamal Adwan hospital told Reuters that bodies and injured people remained trapped under rubble.
He said the destruction of hospitals and lack of medical supplies meant doctors and nurses mostly had no chance of saving people who came in with injuries from air strikes and gunfire.
"Whoever is injured, just lies there on the ground and whoever is killed can't be transported, except by mule-drawn cart," he said.
Israel's decision this week to ban the UN relief agency UNRWA from operating on its territory could have a disastrous impact on humanitarian efforts in Gaza, UN officials said.
The Gaza war began after Hamas, the Palestinian militant group that for years ruled the territory, attacked Israeli towns and villages on October 7, 2023, killing some 1200 people, according to Israeli authorities.
with DPA