The factories, some of which reportedly manufacture household goods, were bombed by Israeli aircraft late on Sunday night.
One factory in Saida's Shwaifat district was still burning on Monday.
Israeli aircraft also hit a petrol station in al-Rumaila, a town just north of Saidon, Aljazeera's correspondent in south Lebanon reported.
There has also been an explosion at a power station in the al-Jiya area of Saida, Aljazeera correspondents said. The cause of the blast was not yet known.
Israel has attacked Lebanon's infrastructure to press the Lebanese government to stop Hezbollah, a Shia political party, from firing rockets into Israel.
Rocket attacks by Hezbollah's armed wing have killed 12 Israeli civilians in the past six days.
Lebanese civilians living near the Israeli border have begun fleeing from their homes after the Israeli military yesterday warned them that it would step up its attacks against Hezbollah positions there
Seventeen people, including nine Lebanese soldiers, have been killed in the latest wave of Israeli airstrikes across Lebanon.
Israel fired missiles at targets in Lebanon early on Monday, killing at least 17 and wounding 53 in a surge of reprisals after Hezbollah rockets hit new targets deep inside Israel.
The soldiers were killed when Israeli aircraft attacked a small fishing port at Abda in northernmost Lebanon next to a main road leading to northern Syria, about 6km from the border.
Witnesses and security officials said 12 others were wounded in the attack that destroyed the position. There was no immediate comment from the military.
Lebanon's army has largely remained on the sidelines of the conflict between Hezbollah and Israel so far, and it was unclear why one of its positions at the far north of the country should be hit.
The road to Syria's northwest was temporarily closed as rescuers evacuated casualties and cleared the rubble.
Warplanes also struck the Beirut international airport premises early on Monday, hitting a fuel storage tank that sent an orange flame billowing high into the sky.
The facility has been closed since Thursday when Israeli missiles punched holes in its runways and set ablaze fuel storage tanks.
Gunboats apparently aiming at a relay station for Hezbollah's al-Manar television missed their target and hit a house in the Kharrub region south of Beirut.
Police said four villagers were killed and 10 wounded.
Lebanese police had no casualty
Israeli warplanes struck repeatedly, hitting neighbourhoods in the eastern city of Baalbek where Hezbollah officials have residences.
Police had no casualty count. Residents reported that the bombardment, up to 12 missiles in six air raids, was the heaviest yet on the city, famous for its Roman ruins. The missiles started several fires.
Along the Beirut-Damascus highway at Taanayel in the central section of the Bekaa Valley in the east, an air raid killed two people and wounded 23 at a commercial compound, police said.
Warplanes also struck at the seaport in Tripoli, Lebanon's second-largest city in the northernmost part of the country. Eight soldiers were wounded, according to witnesses.
It appeared that the Israelis attacked Tripoli and other areas deep inside Lebanon to counter the latest salvo of Hezbollah rockets exploding further south into Israeli territory late on Sunday.
The Hezbollah rockets on the two towns of Afula and Upper Nazareth, about 40km south of the Lebanese border, showed a range farther south than previous barrages.