Call captain makes in ship's toilet (5)
I believe the answer is:
heads
I believe this is a double definition.
'call captain makes' is the first definition.
(a sports captain might call 'heads' in a coin toss)
'ship's toilet' is the second definition.
(term for the toilet on a ship)
'in' is the link.
(Other definitions for heads that I've seen before include "Obverse result of coin-tossing" , "Coin-tossing call" , "School principals" , "a 50-50 chance" , "Goes for" .)