Opinion was divided in the country with some welcoming her coronation as a symbol of diversity, while others accused the competition of favouring “Western beauty standards”.
In the midst of the controversy Japanese magazine Shukan Bunshun published an article accusing her of an affair with a married influencer and doctor.
The man in question has not yet publicly commented on the allegations.
Miss Japan Association, in its initial response to the report last week, defended Ms Shiino, saying she had been unaware the man was married.
However, on Monday, the pageant organisers said she had confessed to knowing about the man’s marital status and apologised for misleading the organisation.
She then resigned her crown.
Ms Shiino also apologised to her fans and the public in a statement, saying her actions had been motivated by fear and panic in response to the report.
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“I am truly sorry for the huge trouble I have caused and for betraying those who supported me,” she said.
The title of Miss Japan will now remain vacant for a year until the next competition.
Ms Shiino won the pageant on 22 January – the first person of European ancestry to take the crown.
She was born in Ukraine before moving with her mother to Japan when she was five and taking on her Japanese stepfather’s last name.
She is fluent in both spoken and written Japanese and became a naturalised citizen in 2022.