Japan has been seen as a safe country in the world. Previous studies that show societal and cultural characteristics have contributed to the comparative low crime rates. Also, the roles of criminal justice system are critical. Today, Japanese society favors a more punitive approach towards offenders. The present study examined which variables of economic factors, socio-structural factors, and deterrence factors affected Japanese crime rates (i.e., homicide, robbery, and larceny), testing for Institutional anomie theory (IAT) and deterrence theory. I conducted visual examination of co-variation with Z-scores and an ARIMA (autoregressive integrated moving average), with Japanese governmental data from 1955 to 2012. The results indicated homicide rates were explained by neither IAT nor deterrence variables. Robbery rates were significantly related with unemployment rates and divorce rates, supporting IAT. Larceny rates were strongly associated with clearance rates, giving support to deterrence theory. Based on the results, practical implications and limitations were discussed.