Captains will have this fish aboard ship (6)
I believe the answer is:
kipper
'captains will have this fish aboard ship' is the definition.
'kipper' can be an answer for 'fish' (type of fish). I am not certain of the rest of the definition.
This is the entire clue.
(Other definitions for kipper that I've seen before include "Cured fish (one having forty winks?)" , "(Fishy) type of tie" , "Cured or smoked herring" , "Breakfast fish (for one who's still asleep?)" , "Dried and smoked herring" .)