He's the Captain of his ship. His word is LAW on his ship. He has a higher officer he reports to. He has a problem like this, it' out of his wheel house. He reports the circumstances to his immediate supervising officer (up the Chain of Command) and requests ORDERS.
Remember, he and his ship have been given a mission. He can offer suggestions but the decision to abort/change mission is up the his boss. Sounds like this Captain DID NOT do that.