The woman, who is in her 20s, aborted the pregnancy when she was told of the potential mix-up at the government-run hospital in Kagawa prefecture, about 330 miles (530 kilometers) southwest of Tokyo.
She is now suing the local government for 20 million yen ($222,000), according to news reports.
Hospital officials apologized for the mistake at a news conference Thursday.
"She was very happy after undergoing such a difficult procedure and becoming pregnant, but unfortunately a mistake had been made," said Yuzo Matsumoto, director of the Kagawa Prefectural Central Hospital.
The hospital has a long history of carrying out such procedures, and this is the first time such a mistake has occurred, hospital spokesman Hajime Morishita said.
"The in vitro procedures are carried out in sequence one after the other, and in this case the eggs from one procedure may have accidentally been left over and used in the following procedure," he said.
In vitro procedures — in which a woman's eggs are removed, fertilized outside the womb, and placed in her uterus to cause a pregnancy — are common in Japan, with hundreds of thousands carried out per year.
The case drew wide attention because bearing and raising children who are not related to the mother is uncommon and has been discouraged by Japanese medical groups.
Surrogate births, in which eggs are removed for fertilization and implanted in another woman, and adoptions are rare in the country.
CLICK HERE to follow Action News on Twitter
CLICK HERE to get Action News on your website
CLICK HERE to find Action News on Facebook
