After 1868 the justice system underwent rapid transformation. The first publicly promulgated legal codes, the Penal Code of 1880 and the Code of Criminal Instruction of 1880, were based on French models, i.e. the Napoleonic code. Offenses were specified, and set punishments were established for particular crimes. Both codes were innovative in that they treated all citizens as equals, provided for centralized administration of criminal justice, and prohibited punishment by ex post facto law. Guilt was held to be personal; collective guilt and guilt by association were abolished. Offenses against the emperor were spelled out for the first time.
Innovative aspects of the codes notwithstanding, certain provisions reflected traditional attitudes toward authority. The prosecutor represented the state and sat with the judge on a raised platform—his position above the defendant and the defense counsel suggesting their relative status. Under a semi-inquisitorial system, primary responsibility for questioning witnesses lay with the judge, and defense counsel could question witnesses only through the judge. Cases were referred to trial only after a judge presided over a preliminary fact-finding investigation in which the suspect was not permitted counsel. Because in all trials available evidence had already convinced the court in a preliminary procedure, the defendant's legal presumption of innocence at trial was undermined, and the legal recourse open to his counsel was further weakened.
The Penal Code was substantially revised in 1907 to reflect the growing influence of German law in Japan, and the French practice of classifying offenses into three types was eliminated. More important, where the old code had allowed very limited judicial discretion, the new one permitted the judge to apply a wide range of subjective factors in sentencing.
After World War II, occupation authorities initiated reform of the constitution and laws in general. Except for omitting offenses relating to war, the imperial family, and adultery, the 1947 Penal Code remained virtually identical to the 1907 version. The criminal procedure code, however, was substantially revised to incorporate rules guaranteeing the rights of the accused. The system became almost completely accusatorial, and the judge, although still able to question witnesses, decided a case on evidence presented by both sides. The preliminary investigative procedure was suppressed. The prosecutor and defense counsel sat on equal levels, below the judge. Laws on indemnification of the wrongly accused and laws concerning juveniles, prisons, probation, and minor offenses were also passed in the postwar years to supplement criminal justice administration.
After identifying a suspect, police have the authority to exercise some discretion in determining the next step. If, in cases pertaining to theft, the amount is small or already returned, the offense petty, the victim unwilling to press charges, the act accidental, or the likelihood of a repetition not great, the police can either drop the case or turn it over to a prosecutor. Reflecting the belief that appropriate remedies are sometimes best found outside the formal criminal justice mechanisms, in 1990 over 70 percent of criminal cases were not sent to the prosecutor.
Prosecution can be denied on the grounds of insufficient evidence or on the prosecutor's judgment. Under Article 248 of the Code of Criminal Procedure, after weighing the offender's age, character, and environment, the circumstances and gravity of the crime, and the accused's rehabilitative potential, public action does not have to be instituted, but can be denied or suspended and ultimately dropped after a probationary period. Because the investigation and disposition of a case can occur behind closed doors and the identity of an accused person who is not prosecuted is rarely made public, an offender can successfully reenter society and be rehabilitated under probationary status without the stigma of a criminal conviction.
Institutional safeguards check the prosecutors' discretionary powers not to prosecute. Lay committees are established in conjunction with branch courts to hold inquests on a prosecutor's decisions. These committees meet four times yearly and can order that a case be reinvestigated and prosecuted. Victims or interested parties can also appeal a decision not to prosecute.
The judge conducts the trial and is authorized to question witnesses, independently call for evidence, decide guilt, and affix a sentence. The judge can also suspend any sentence or place a convicted party on probation. Should a judgment of not guilty be rendered, the accused is entitled to compensation by the state based on the number of days spent in detention.
Criminal cases from summary courts, family courts, and district courts can be appealed to the high courts by both the prosecution and the defense. Criminal appeal to the Supreme Court is limited to constitutional questions and a conflict of precedent between the Supreme Court and high courts.
The criminal code sets minimum and maximum sentences for offenses to allow for the varying circumstances of each crime and criminal. Penalties range from fines and short-term incarceration to compulsory labor and the death penalty. Heavier penalties are meted out to repeat offenders. Capital punishment consists of death by hanging and can be imposed on those convicted of leading an insurrection, inducing or aiding foreign armed aggression, arson, or homicide.
Many Western human rights organizations alleged that the high conviction rate is due to rampant use of conviction solely based on confession, notwithstanding Article 38 of Japan's Constitution,which categorically requires that "no person shall be convicted or punished in cases where the only proof against him is his own confession," and that no person can be convicted unless accompanied by other evidence to corroborate that confession.
Due to the lack of a jury system, the Japanese justice system (along with all other civil law jurisdictions) is said to be very bureaucratic and predictable. Because judges work under a fairly uniform system of evidence and procedure, which is indirectly supervised by Ministry of Justice, the district prosecutor knows exactly the types of evidence which are needed to secure a conviction from a judge. Consequently, failing to secure a conviction would be seen as serious failure in his judgement for pressing charges in the first place and even a single failure would have a serious negative impact on the career of a prosecutor. One of the consequence of this arrangement is that prosecutor rarely press charge involving rape or assault involving acquaintance.
While given the predictable nature of court proceedings, judges are often assessed by the efficiency (i.e. speed) of court proceedings. Moreover, unlike common-law jurisdictions, the most adversarial part of court proceedings between prosecutors and the defense focus on sentencing.
The Japanese criminal justice system, despite retaining the death penalty, is relatively lenient in sentencing by the standard of other developed countries. Outside capital cases, many of those sentenced to life sentences are paroled within 15 years. Those convicted of less heinous murder and manslaughter are likely to serve less than 10 years. Those convicted of rape will often serve less than two to five years. It is even possible for someone convicted of murder to serve a suspended sentence if the defense successfully argues for mitigating circumstances. Moreover, in Japanese criminal proceedings the conviction and sentencing phase are separate. In common law jurisdictions, prosecutors make cases not just for the guilt of the accused, but also for the punishment. In the Japanese criminal justice system, these are distinct phases. The court proceedings first determine guilt, then a second proceeding takes place to determine the sentence. Prosecutors and defense teams argue each phase. Defense lawyers, given the predictability of the outcome in term of guilt once the charge is brought, together with leniency of punishment (except in death penalty cases), often advise the accused to confess their guilt in trial. Remorse is seen as a mitigating factor which tends to bring reduced sentences.
During 1970s, a series of reversals of death penalty cases brought attention to the fact that some accused, after intensive interrogation, signed as-of-yet unwritten confessions, which were later filled in by investigating police officers. These coerced confessions, together with other circumstantial evidence, often convinced judges to (falsely) convict.
Currently the Japanese Federation of Bar Associations is calling for the entire interrogation phase to be recorded to prevent similar incidents occurring. The International Bar Association, which encompasses the Japanese Federation Of Bar Associations, cited problems in its "Interrogation of Criminal Suspects in Japan". Furthermore, the office of prosecutors has reversed their opposition to this proposal. Part of the reason is their worry that, without the credibility of confessions supported by electronic recording, the soon-to-be-introduced jury system may refuse to convict in a case other offered evidence is weak.
J. Mark Ramseyer of Harvard Law School and Eric B. Rasmusen of Indiana University argue in their paper ("Why Is the Japanese Conviction Rate So High?") that the conviction rate in Japan is high due three factors:
Temple University professor and author Ivan Hall asks whether Ramseyer's ready defence of Japanese institutions may be due to a conflict of interest—Ramseyer holds the million-dollar Mitsubishi Chair at Harvard Law School.
In October 2007, the BBC published a feature giving examples and an overview of "'Forced confessions' in Japan". The case was called "志布志事件". In addition, Hiroshi Yanagihara, who was convicted in November 2002 for attempted rape and rape due to forced confession and the identification by the victim despite alibi based on phone record, was cleared in October 2007 when the true culprit was arrested on unrelated crime. The two cases damage the credibility of Japanese Police.