Trained assassin in prison in Japan (5)
I believe the answer is:
ninja
'trained assassin' is the definition.
(I've seen this before)
'in prison in japan' is the wordplay.
'in' indicates the answer is hidden within the clue.
'NINJA' can be found hidden inside 'prison in japan'.
(Other definitions for ninja that I've seen before include "Old Japanese hired assassin" , "old mercenary" , "14th-century Japanese soldier of fortune" , "Stealthy Japanese spy" , "Expert in espionage" .)