The incident happened on Tuesday in the city of Tokushima, police said. The 39-year-old driver was playing the game behind the wheel and hit two pedestrians, and one died from her injuries.
"We express our deep condolences to the family and acquaintances," Niantic, the developer of Pokemon GO, said in a statement. "We are still looking into the details of the incident. We will take any necessary steps following the completion of an investigation."
Pokemon GO became a social phenomenon following its debut last month, with parks and streets in cities from New York to Tokyo filled with people chasing virtual pocket monsters on their phones.
In many public areas in Japan, signs have gone up asking people not to walk while using their smartphones. While the number of daily active users appears to have declined after hitting a peak, there are still more than 30 million people playing the game each day.
The driver of the car in Tuesday's incident, who was taken into custody after the accident, told police that he had been playing Pokemon GO and hadn't seen the two pedestrians.
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