All on board the stricken boat - which came ashore near the town of El Dheer in Galgaduud region - were led away by masked fighters from the group to unknown location, a witness speaking on condition of anonymity because of fear of retaliation by the group said.
Several of those on board were thought to be Iranian nationals. The boat is said to have been carrying fuel.
The group have not commented on the incident.
It is not the first time the group has seized a boat.
Early this year the group seized a boat ferrying khat - a mild leafy narcotic plant chewed in East Africa - near the Somali port town of Barawe in Lower Shabelle region.
The group is fighting the internationally recognised government in Mogadishu to impose a strict version of Islamic law in the horn of Africa country.
By Al Jazeera