The Lebanese navy is holding a Sierra Leone-registered ship and says it has confiscated a large consignment of arms and ammunition it was carrying.
The 11 crew members were detained after three shipping containers full of heavy and light weapons were found on the Lutfallah II.
The BBC's Jim Muir in Beirut says it is believed the consignment was destined for the rebels in Syria.
Some of the arms were labelled as Libyan, says Reuters news agency.
The ship's owner told Reuters it was due to unload in Tripoli, northern Lebanon.
Milos Strugar, a spokesman for the United Nations Interim Force in Lebanon (Unifil) which assists Lebanon in preventing illegal arms entering the country, confirmed to the BBC that it was bound for a Lebanese port.
Tripoli is a hotbed of support for the Syrian opposition, and the authorities in Damascus have frequently complained about arms being smuggled from the areas into the country, our correspondent says.
Violence has fallen in Syria since a ceasefire was put in place, but activist groups still counted some 40 deaths in fighting across the country over the weekend.
The dead included 26 civilians killed by government forces, said the UK-based Syrian Observatory for Human Rights.
Attacks from sea
Russia has accused Libya of supporting the Syrian rebels and providing them with weapons.
Lebanese media say there was light, medium and heavy weaponry in the consignment.
The ship is reported to have begun its voyage from Libya, stopped off in Alexandria in Egypt, and then headed for the port of Tripoli in northern Lebanon before it was intercepted.
It is now being held at the port of Salaata near Beirut. AP news agency reported that the containers had been placed on Lebanese army flatbed trucks and taken away.
They are now being held under lock and key at an army base.
The owner of the Lutfallah II told Reuters that he was told the ship was carrying engine oil, and was unaware of any weapons. "The law doesn't allow me to open and inspect the containers," he said.
He said the ship was originally asked to carry 12 containers of "general cargo" from Libya to Lebanon. After three days of delay it left only carrying the three containers, he told Reuters.
On Saturday Syrian rebel gunmen in inflatable dinghies attacked a military unit on the Mediterranean coast, with deaths on both sides, state media report.
It is thought to be the first rebel assault from the sea. The violence comes despite a shaky ceasefire in force since 12 April.
Syria's official news agency Sana said a military unit had foiled a "terrorist attempt" to infiltrate the country overnight by boat in Latakia province.
The UN currently has about 15 observers in Syria monitoring a shaky ceasefire, which came into force on 12 April, and hopes to have the full advance team of 30 in place by Monday.
Violence has been continuing despite the truce.
On Thursday UN Secretary General Ban Ki-moon warned that Syria's government was "in contravention" of a UN- and Arab League-backed peace plan.
Mr Ban has demanded that Damascus comply with the peace plan brokered by international peace envoy Kofi Annan without delay.
The Security Council has approved the deployment of up to 300 monitors. Norwegian Maj Gen Robert Mood, who is to lead the team, arrived in Damascus on Sunday.
"To achieve the success of Kofi Annan's six-point plan... I call on all to stop the violence and to help us on a continued cessation of armed violence in all its forms," Gen Mood told reporters.