The 6-member team will work around the town of Imphal, where the British and Japanese army clashed in 1944.
To date, the battle, which has been dubbed "Battle of Imphal", has been seen as one of the greatest battles of the Second World War.
It was voted Great Britain's "Greatest Battle" by the nation's Army Museum.
According to media reports, Chief Minister N. Biren Singh has informed the press that advanced preparations were made to welcome the team and that all help will be accorded them.
Earlier, similar Japanese teams had excavated bones and other remains from battlefields in and around Manipur. However, this time, the team would incinerate the bones before sending the ashes back to Japan.
Additional Chief Secretary, Home, Suresh Babu revealed that the Japanese team would stay in Manipur for eight days.
He said, "...team members shall visit Ukhrul, Imphal East, Bishnupur and Imphal West districts where fierce battles were fought during World War II. Japan hopes to find several bones. Adequate security arrangements have been made for them."
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