Twenty strikes hit the governorate, killing 30 people and injuring 35, Khodr has said.
"The historic quarter of Manshiya near the temple complex of Baalbek has been targeted by the Israeli air force," the official said.
According to Khodr, one of the missiles struck a parking area near the ancient complex.
He stressed that Wednesday's strikes were the closest to the Roman temples.
Baalbek, formerly known as Heliopolis, was an important holy city in the Roman Empire. The city is known worldwide for the temples of Jupiter and Bacchus, which are on the UNESCO World Heritage List, as well as several unique megaliths.