The strikes came more than 24 hours after Israel carried out similar raids deep inside east Lebanon and as tensions mounted in the wake of the Israeli killing of a top Hezbollah commander.
"Israeli enemy strikes on the Bekaa" valley killed one person "and wounded 20 others", the health ministry said in an updated toll.
The statement said one person was in critical condition while "eight children and a pregnant woman were moderately wounded".
A Hezbollah source, requesting anonymity, said several strikes hit east Lebanon near the city of Baalbek, including the village of Nabi Sheet, without specifying what was targeted.
A source from a local hospital told AFP that five children no older than 10, all from the same family, were among the wounded.
The strikes around midnight came after similar raids in the Bekaa region on Monday evening that Israel said targeted "Hezbollah weapons storage facilities".
They also came as Hezbollah said four of its fighters had been killed, after the health ministry said Tuesday that four people died in Israeli strikes in the southern border village of Dhayra.
The Iran-backed Hezbollah, an ally of Palestinian armed group Hamas, has traded near-daily cross-border fire with Israeli forces since the Gaza war began in October.
The violence has largely been restricted to the Lebanon-Israel border area, although Israel has repeatedly struck the country's eastern Bekaa valley near the border with Syria where Hezbollah also has a strong presence.
Hezbollah claimed a string of attacks on Israeli troops and positions on Tuesday, including sending barrages of Katyusha rockets at several north Israel military positions in stated retaliation for Israeli strikes, including in Dhayra.
The Shiite Muslim movement also said it launched "squadrons of explosive-laden drones" and "intense rocket barrages" at several Israeli positions in the annexed Golan Heights in response to Monday night's strikes in the Bekaa valley.
- Health workers 'targeted' -
The Israeli military in separate statements said a total of around 115 "projectiles" were identified crossing from Lebanon.
It also said that "numerous suspicious aerial targets were identified crossing from Lebanon", with air defences intercepting some of them.
No injuries were reported, though the military said the incidents sparked fires in some areas.
The military also said air forces struck projectile launchers and several "Hezbollah military" structures in south Lebanon.
Lebanon's health ministry said three emergency personnel from the Hezbollah-affiliated Islamic Health Committee were hurt Tuesday when the Israeli military "targeted them" in south Lebanon, causing "significant damage to the ambulance they were travelling in".
The ministry "condemned in the strongest terms the repeated targeting of health workers in south Lebanon".
Several militant groups in Lebanon operate health centres and emergency response operations, with at least 21 rescue workers killed since October, according to an AFP tally.
Fears of a major escalation have mounted since Hezbollah and Iran vowed to respond to twin killings blamed on Israel late last month.
An Israeli strike on Beirut's southern suburbs killed a top Hezbollah commander, Fuad Shukr, shortly before an attack in Tehran blamed on Israel killed Hamas political leader Ismail Haniyeh.
The cross-border violence has killed some 590 people in Lebanon, mostly Hezbollah fighters but also including at least 128 civilians, according to AFP's tally.
On the Israeli side, including in the annexed Golan Heights, 23 soldiers and 26 civilians have been killed, according to army figures.