Saudi destroys bomb-laden boat off Red Sea port
"A bomb-laden unmanned (vessel) was intercepted and destroyed this morning," the ministry said in a statement, published by the official Saudi Press Agency.
"Naval units were able to detect and monitor the activity of the bomb-laden (boat) in the Red Sea waters off the shores of Yanbu."
No group has so far claimed responsibility for the incident, which the ministry said was under investigation.
The incident comes as fighting escalates in neighbouring Yemen between Saudi-backed government forces and Iran-aligned Huthi rebels.
Huthi insurgents are ramping up a bloody offensive to seize the oil-rich Marib region, the Yemeni government's last stronghold in northern Yemen.
The rebels have used bomb-rigged boats in the past to target the kingdom.
Last week, Greece said it will transfer a Patriot missile battery to Saudi Arabia to protect its critical energy infrastructure, as the Gulf kingdom grapples with the growing attacks.
Maritime security firm Dryad Global said it had received reports that a ship had been "attacked" off Yanbu.
But the firm later said the ship was "not involved in the incident" and it will continue to investigate.