Police suspect Hiroe Miyata, aged in her 60s, was interred last month in Dhaka under a fake identity after officers examined records at the Muslim graveyard.
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Authorities began investigating after the woman's mother in Japan reported her missing to the Japanese embassy in Dhaka on November 19.
"We are treating this as a murder" investigation pending a post-mortem to determine cause of death, one police officer told AFP on condition of anonymity.
Another police official said the woman had been living and working in Dhaka for the last 10 years.
"She died in mysterious circumstances," the official, who also declined to be named because of the preliminary nature of the case, told AFP, saying the woman was buried under a Muslim name.
"We've sought a court order to exhume the body and determine the reason for her death."
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Private television Channel 24 said three people have been arrested over her death but police refused to confirm this.
A Japanese embassy spokesman declined to comment.
The probe follows the murders of a Japanese farmer and an Italian aid worker in separate incidents in Bangladesh in recent months, attacks claimed by the Islamic State.
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An Italian priest was shot and seriously injured last week.
The Bangladesh government says the militant group has no presence in the Muslim-majority country, while police suspect a local banned militant outfit was responsible.
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