The octogenarian spent 46 years on death row for a quadruple murder in 1966 but a court acquitted him in September, ruling that evidence had been fabricated.
Last month the local police chief came to Hakamada's home to say he was sorry and on Wednesday it was the turn of regional chief prosecutor Hideo Yamada.
"We feel terribly remorseful that Mr Iwao Hakamada was put into legally unstable conditions for a significantly long period of time, forcing you and (your sister) Hideko to face hard times that are barely possible to put into words," local media quoted Yamada as saying as he bowed in apology.
His sister Hideko, 91, who often speaks for her brother, said they were "extremely happy that he was found innocent. Thank you for coming today."
Japan is the only major industrialised democracy other than the United States to retain capital punishment, a policy that has broad public support.
Hakamada, 88, is the fifth death row inmate granted a retrial in Japan's post-war history. All four previous cases also resulted in exonerations.
Just a week after his acquittal, Japan's then justice minister Hideki Makihara said abolishing the death penalty would be "inappropriate" as "heinous crimes continue to occur."
He pledged to be "cautious and extremely sincere" when making the decision to sentence someone to death, according to Nippon Television's online media.
