Captain could create stink on ship (4)
I believe the answer is:
boss
'captain' is the definition.
'stink on ship' is the wordplay.
'stink' becomes 'bo' (body odour).
'on' says to put letters next to each other.
'ship' becomes 'ss'.
'bo'+'ss'='BOSS'
'could create' is the link.
(Other definitions for boss that I've seen before include "Head honcho" , "Bully" , "Informal employer or superior" , "Stud; employer" , "Team manager" .)