Lebanese officials say Sunni cleric Hussam al-Sabbagh is accused of recruiting fighters and sending them across the border into Syria.
He is also accused of having links to al-Qaeda and the militant group Fatah al-Islam.
The cleric was arrested after being stopped at a checkpoint by Lebanese soldiers acting on several arrest warrants.
Angry supporters were later reported to have exchanged fire with soldiers. A suspect of Swedish nationality was killed in the same raid.
Who is Hussam al-Sabbagh?
Hussam al-Sabbagh has been described as the "emir of al-Qaeda in Tripoli".
Hussam al-Sabbagh, who is believed to have previously called for jihadis to attack Australian soldiers in Afghanistan, commands an armed force of at least 300 jihadi fighters, according to security reports.
Sabbagh is believed to have arrived in Australia about 1987 after fleeing Lebanon and Syrian security services and worked in construction.
He returned to Lebanon in 2004 but did not come to prominence until 2012.
Another terror suspect, Omar Khodor, who is in the custody of Lebanese army intelligence, has reportedly confessed that he was on his way to meet with Sheikh Hussam Sabbagh in north Lebanon to hand him funds to be used in preparing car bombs.
Before his arrest at the weekend, Sabbagh had denied the allegations.
Sabbagh also denies having links to al-Qaeda, despite having been described in reports as the terror group's "emir" or commander in Tripoli, the largest city in northern Lebanon and about 85 kilometres north of the capital Beirut.
While it's believed he commands about 300 fighters, some reports have suggested his forces are twice that number.
According to the website, Al Akhbar, Sabbagh opposed jihad in Australia despite its participation in the war in Afghanistan, because Australia was a country that "gave us shelter when none did".
Instead, the website said, he called on jihadis to fight against Australian soldiers in Afghanistan.
Sabbagh's arrest along with one of his bodyguards, angered the cleric's supporters who later exchanged gun fire with the army in the Sunni-majority district of Bab al-Tebbaheh.
The Australian government has been contacted for comment.
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