Captain missing first bit of smoked fish (6)
I believe the answer is:
kipper
'smoked fish' is the definition.
(I've seen this before)
I don't understand the rest of the clue.
(Other definitions for kipper that I've seen before include "One not awake" , "Breakfast fish (for one who's still asleep?)" , "Cured fish (one having forty winks?)" , "One smoked" , "One drops off" .)