Scientists have confirmed that bones found in a grave on a building site in Tokyo belong to an Italian missionary who died in prison more than three centuries ago. 

DNA tests have confirmed that the remains are those of Giovanni Battista Sidotti, AFP reported.

The missionary's remains are one of three sets of bones discovered two years ago in the parking lot of a block of flats which was once a prison called Kirishitan Yashiki, or the Christian Mansion.

Researchers from Japan's National Museum of Nature and Science spent six months piecing together the fragments of bone. 

DNA analysis on a tooth showed it to be of Italian extraction. At the time just two Italians were in the country, Sidotti and the Jesuit missionary priest Father Giuseppe Chiara. The latter was cremated after he died aged 84 so it could not be his skeleton.

Some of the events of that era are soon to become the subject of a Hollywood film centred on faith, God and the persecution of Christian missionaries in Japan. 

The Japanese writer Shusaku Endo wrote a best-selling novel based on the life of Father Chiara, Silence, which is currently being turned into a film by director Martin Scorsese. It will star "Spiderman" Andrew Garfield along with Adam Driver and Liam Neeson.

A decree banned Christianity in Japan in 1614. Sidotti, disguised as a Samurai warrior, arrived in 1708, having travelled there in an attempt to help the many Christian priests facing torture in Japan. He died in prison in 1714, aged 47. He had developed a close friendship with the Confucian philosopher Arai Hakuseki who was influenced by Sidotti in at least two of his most important works.

It is possible he might one day have been released from prison, had he not refused to give up his efforts to convert his guards.