Fish made captain lose head (6)
I believe the answer is:
Here is my best explanation:
'fish' is the definition.
(kipper is a kind of fish)
'captain lose head' is the subsidiary indication.
'captain' becomes 'skipper' ('skipper' can be a synonym of 'captain').
'lose head' means to remove the first letter.
'skipper' with its initial letter taken away is 'kipper'.
'made' is the link.
(Other definitions for kipper that I've seen before include "Cured or smoked herring", "Dried and smoked herring", "One not awake", "Narcoleptic", "One smoked", "A smoked herring", "(Fishy) type of tie", "has been caught napping", "Herring" and "being in bed?".)