Former Tokyo medical school site is linked to Unit 731, branch of imperial army which used prisoners in germ warfare programme

Authorities in Japan have begun excavating the former site of a medical school that may contain the remains of victims of the country's wartime biological warfare programme.

The school has links to Unit 731, a branch of the imperial Japanese army that conducted lethal experiments on prisoners as part of efforts to develop weapons of mass destruction.

The Japanese government has previously acknowledged the unit's existence but refused to discuss its activities, despite testimony from former members and growing documentary evidence. In 2002 a Japanese court said Tokyo was under no obligation to compensate victims.

The government agreed to launch a ¥100m (£741,000) investigation after Toyo Ishii, a former nurse, said she had helped bury body parts on the site as the US occupation forces moved into Tokyo at the end of the second world war. Officials said so far there was no evidence the site had been used for experiments.

"We are not certain if the survey will find anything," Kazuhiko Kawauchi, a health ministry official, told Associated Press. "If anything is dug up, it may not be related to Unit 731."

Experts believe that if the excavation yields physical evidence that Japan conducted experiments on live humans, the government would face pressure to discuss the country's wartime conduct. "If bones or organs with traces of live medical experiments are found, the government would have to admit a wartime medical crime," said Yasushi Torii, head of a group that has been investigating the case for decades. "This is a start, although we will probably need more evidence to prove Unit 731's involvement."

Ishii, 88, broke her 61-year silence in 2006, claiming that she and colleagues had been ordered to bury numerous corpses, bones and body parts in the grounds following Japan's surrender in August 1945.

The then conservative government met with Ishii five years ago over her claims and pledged to pursue the case.

However, authorities held off on excavation until residents had been relocated and their apartments demolished last year. The current left-of-centre administration, which took office in 2009, has shown greater willingness to examine the darker episodes in Japan's wartime history.

The site in Tokyo's Shinjuku district is close to another where the mass graves of dozens of people who may have been victims of wartime experiments was uncovered in 1989.

Investigators concluded, however, that the remains, which included skulls with holes drilled through them or sections removed, were not connected to Unit 731 and that there was no evidence of criminal activity.

The health ministry concluded that the remains were those of non-Japanese Asians that had been used in "medical education" or recovered from war zones for analysis in Japan.

Unit 731, based in Harbin in northern China, conducted experiments on tens of thousands of mostly Chinese and Korean prisoners, and a small number of Allied prisoners of war. Some historians estimate up to 250,000 people were subjected to experiments. The remains of some are thought to have been transported from China to Tokyo for analysis.

According to historical accounts, male and female prisoners, named "logs" by their torturers, were subjected to vivisection without anaesthesia after they had been deliberately infected with diseases such as typhus and cholera. Some had limbs amputated or organs removed.

Leading members of the unit were secretly granted immunity from prosecution in return for giving US occupation forces access to years of biological warfare research. Some went on to occupy prestigious positions in the pharmaceutical industry, health ministry and academia.

Human guinea pigs

Japan's push into China began in 1931, and had become an occupation of large areas of the country by 1937, the year of the notorious Nanking massacre, in which, by some historical estimates, between 250,000 and 300,000 people in the city were killed. Those figures are disputed by some Japanese historians, who say the death toll was lower.

Unit 731 began conducting germ warfare experiments from its headquarters in Harbin, north-east China, in the mid-1930s, using human guinea pigs to develop biological weapons to assist Japan's push into regions in the south-east.

In 2004, a Chinese survivor described to the Guardian how his home on Zhejiang province, south-east China, had been attacked by plague-inflected fleas dropped by Japanese occupation forces. Records show that hundreds of thousands of Chinese civilians were infected with the plague and other diseases.

As Japan confronted defeat in the summer of 1945, the unit's leader, Lieutenant General Shiro Ishii, told researchers to take their secrets to the grave and ordered his troops to demolish the unit's compound in Harbin.

But some former members of Unit 731 have come forward to discuss the past. They include Akira Makino, a former doctor who in 2006 said he had been ordered to conduct experiments on condemned men while stationed on the island of Mindanao in the Philippines.