Nagasaki City Mayor Iccho Itoh, 61, who was shot at near his office, died in the small hours of Wednesday.
The gunman Tetsuya Shiroo, the 59-year-old senior member of Japan's largest crime syndicate, the Yamaguchi-gumi, was arrested on the scene immediately after shooting twice at the mayor's back. Later he made full confessions.
The police are still investigating the motives for the crime.
It is assumed that the gangster killed the mayor as he was angry with the local authorities for his car has been damaged because of construction works in the city.
Iccho Itoh was shot dead while campaigning in his bid for re-election for a forth term as mayor.
He first fell in clinical death. Unfortunately the doctors did not manage to save his life.
That was the second assault against a mayor of Nagasaki. The first one occurred in 1990, when ultra right extremists shot at the then mayor.