The clashes prompted the Lebanese army to issue a statement pledging "decisive and firm" action to prevent the Syrian conflict from spilling over into Lebanon.
The violence began after troops detained Imad Ahmed Jumaa, a Syrian man accused of belonging to Al-Qaeda's Syrian affiliate, Al-Nusra Front, in the Arsal region of eastern Lebanon by the Syrian border.
The army said in a statement that it had detained Jumaa at noon, and security sources and local residents said unidentified gunmen began to surround local army checkpoints shortly afterwards.
NNA later said two Lebanese soldiers were killed in attacks on checkpoints, and the army acknowledged "deaths and injuries" among its ranks, but without giving further details.
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In a statement, the army warned of the seriousness of the situation in Arsal, a predominantly Sunni Muslim town where support for the uprising across the border in Syria runs strong.
"The army will be decisive and firm in its response and will not remain silent as foreigners try to turn our land into a field for crime and terrorism, murder and kidnapping," it added.
The army also confirmed reports that gunmen had briefly captured soldiers who its forces were able to later free.
Local media reported that the gunmen were holding a number of policemen, but there was no immediate confirmation.
The army deployed additional forces, including two helicopters, to the region in the wake of the clashes, which were continuing early Saturday evening.
Syria's army has also launched regular air raids and shelled the area around Arsal, saying it is targeting rebels who have holed up in the mountainous region surrounding the border town.