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Michiko's husband Akihito formally stepped down as emperor in April, the first abdication for 200 years in the world's oldest monarchy.
Her operation began Sunday morning "as scheduled" at the University of Tokyo Hospital, the agency official said.
It will take some hours to finish her surgery and the agency is scheduled to announce results later in the day, according to local media.
Akihito and daughter Sayako Kuroda, a former princess who left the royal household to marry a commoner, visited the hospital to see Michiko before the operation.
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Akihito and Michiko are known for dramatically modernising the tradition-bound monarchy, bringing themselves closer to the public and boosting popular support for the household.
The first commoner ever to marry an imperial heir, Michiko was born in 1934 in Tokyo and attended the exclusive all-girls Christian Sacred Heart School before studying English literature at its university.
She gave birth to now-Emperor Naruhito in 1960 and her second son, Prince Akishino, was born in 1965.
Michiko and her husband also came to be known for their presence at the side of survivors of disasters, especially after the 2011 tsunami that wrecked large parts of eastern Japan.