Junior officer in navy, on vessel working late (9)
I believe the answer is:
subaltern
'junior officer' is the definition.
(I've seen this before)
'navy on vessel working late' is the wordplay.
'navy' becomes 'rn' (abbreviation for Royal Navy).
'on' means one lot of letters go next to another.
'vessel' becomes 'sub' (sub is a kind of vessel**).
'working' is an anagram indicator.
'late' anagrammed gives 'alte'.
'sub'+'alte'='subalte'
'rn' after 'subalte' is 'SUBALTERN'.
'in' is the link.
(Other definitions for subaltern that I've seen before include "Junior officer" , "Lesser official" , "Army officer below the rank of captain" .)