"The boat was heading towards the (Red Sea) port of Al-Mukha" and the arms "were destined for the Huthi rebels in Saada," the northern stronghold of the Shiite fighters, the Yemeni security official told AFP.
Yemeni coast guard in coordination with the US navy last month intercepted the ship in the Arabian Sea, authorities have said.
The vessel "came from Iran and was carrying arms and explosives among them surface-to-air missiles SAM-2 and SAM-3," state news agency Saba reported on Sunday, adding that the crew of eight Yemeni nationals were being questioned.
The ship was stopped on January 23 in Yemeni territorial waters and flew several fake flags, authorities have said.
An offshoot of Shiite Islam, Zaidis are a minority in mainly Sunni Yemen but form the majority in the mountainous north.
From 2004 the Huthis fought six wars with central government forces before signing a truce in February 2010. The rebellion claimed thousands of lives.
The government accuses the rebels of being backed by Shiite-dominated Iran, charges which the Zaidis deny.