Japan's third-largest city (5)
I believe the answer is:
osaka
'japan's third-largest city' is the definition.
(I've seen this in another clue)
This is the entire clue.
(Other definitions for osaka that I've seen before include "Japanese port city" , "S. Japan port, bay" , "Large city and port in Japan" , "Major port and commercial and industrial centre on Honshu" , "Japanese port, on Honshu" .)