The woman, in her 40s, last year went for a mammogram at a hospital in the western city of Okayama and was told there was a possibility she had breast cancer.
Doctors removed her breast. But a detailed examination of the tissue showed that she had a mastopathy, which includes symptoms similar to those of cancer but does not require surgery.
"We deeply regret that we caused the patient irreparable harm. We will take measures so that this will never happen again," Tatsuya Itoshima, director of the Saiseikai General Hospital, told a televised news conference.
An internal investigation found that the woman's identification number and tissue sample were mixed up with those of a genuine cancer patient who had undergone testing the same day as the healthy woman.
It was not immediately known whether the patient has received compensation for the mishap. The genuine cancer patient later also had her breast removed.