The third largest city in Japan (5)
I believe the answer is:
osaka
'the third largest city in japan' is the definition.
(I've seen this before)
This is all the clue.
(Other definitions for osaka that I've seen before include "Japanese port, on Honshu" , "Kinki's capital" , "Japan's third-largest city" , "Port city of southern Honshu" , "Japanese metropolis" .)