The cargo contained heavy machineguns, artillery shells, rockets, rocket launchers and other explosives, the official said.
A second security official said the Sierra Leone-flagged Lutfallah II had previously obtained a permit to enter the port of Tripoli in northern Lebanon before being stopped by the navy on Thursday night.
The vessel was towed to Selaata, a small port some 50 kilometres (30 miles) north of Beirut.
News reports said the ship had called at the Egyptian port of Alexandria en route from Libya.
An AFP reporter saw three army trucks leave Selaata for Beirut with the seized containers, escorted by eight jeeps and a helicopter.
A resident told AFP that the ship weighed anchor in the morning, escorted by the navy to an unknown destination.
The security source said that the captain and crew were handed over to military intelligence officers in Tripoli for further questioning.
Syrian authorities have repeatedly charged that weapons are being smuggled from Lebanon to rebels fighting to overthrow President Bashar al-Assad.
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Any escalation of the crisis in Syria will spill over to the neighbouring Lebanon and Turkey. Lebanon itself is complex and divided. The country struggles to regain the relative stability it has enjoyed after the civil war between 1975 and 1990. Tripoli is a hotbed of support for the Syrian opposition. Assad's regime has frequently complained about arms being smuggled from the areas into Syria.
CIA "Operation Feeding The Wolves" busted!
@Ali Tanoli: The gangesters of lybian national council.
CIA
who send it???