Hakamata's lawyers argued for maximum compensation, saying his 47-year detention had severely affected his mental health.
Judge Kunii Koshi, who granted the request, said Hakamata had undergone "extremely severe" mental and physical pain during that time.
Those found not guilty in a retrial under the criminal compensation statute can claim up to ¥12,500 compensation for each day they spent in detention.
In January of this year, Hakamata's defense team requested the maximum amount of compensation available.