Pardons, Clemencies, Amnesties, etc have not been granted in Japan since the 1970's. This is a shame and the reason why they have fallen into hibernation is unknown. The authority to grant is based in two places in the constitution.
第１章 天 皇
The Emperor shall, with the advice and approval of the Cabinet, perform the following acts in matters of state on behalf of the people:
(6) Attestation of general and special amnesty, commutation of punishment, reprieve, and restoration of rights
第５章 内 閣
The Cabinet shall, in addition to other general administrative functions, perform the following functions:
(7) Decide on general amnesty, special amnesty, commutation of punishment, reprieve, and restoration of rights.