The Justice Ministry said Friday that a special probe into suspicious prisoner deaths between 1993 and 2002 has found evidence of abuse by guards in just two of the 1,566 cases under scrutiny.

The two cases involve fatal abuse of inmates at Nagoya Prison over the past two years — cases that came to light in the fall.

It was in the wake of those revelations that the ministry formed a special investigation team of five prosecutors and five ministry officials.

It launched the probe in April into all prisoner deaths from 1993 to 2002 other than executions.

While the ministry had reportedly acknowledged that “systematic and organizational” problems at prisons may have been behind the Nagoya cases, it effectively ruled that these cases were exceptional.

Seven former Nagoya Prison guards are currently on trial at the Nagoya District Court over the fatal abuse of two inmates in December 2001 and May 2002. The incidents came to light after another Nagoya Prison inmate was severely injured by guards in September.

According to internal ministry records disclosed earlier this year, at least five prisoners died after being bound in controversial leather restraining devices in padded cells, the same practice used in one of the Nagoya deaths.

The ministry’s final report, however, concludes that it is unlikely there is a causal link between the death of prisoners and the use of the handcuffs, selectively referring to opinions given by medical experts.

For instance, the report contains the conclusion that an inmate’s death at Osaka Prison in 1997 was not linked to the use of the restraining device, just because it took around a day before the inmate died after being restrained.

But the report also denies that use of the leather device killed another inmate at Kyoto Prison in 1993 — although he died just 90 minutes after being restrained.

In another case, the report judges that a detainee at Kawagoe Juvenile Prison in 1995 died from choking on his own vomit soon after he was physically suppressed by guards and placed in the device.

But the report concludes that their actions and the death were not connected as the prisoner began vomiting “more than two or three minutes after the action of suppression.”

Meanwhile, the ministry filed a criminal complaint with the Hachioji branch of the Tokyo District Court on Friday, claiming that a guard at Fuchu Prison in Tokyo either discarded or lost portions of death records tied to nine deceased inmates at the prison. No specific suspect was named.

The ministry also determined that two prisoners may have died because of inappropriate medical treatment and reported these cases to the Supreme Public Prosecutor’s Office.

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