Justice Minister Yoko Kamikawa said a report on the March death of 33-year-old Wishma Sandamali concluded she received inadequate treatment as her health deteriorated.
Sandamali was detained for overstaying her visa after seeking police protection, reportedly to escape an abusive relationship.
She reportedly complained repeatedly of stomach pain and other symptoms starting in January, and campaigners allege she was given inadequate medical care.
“I express my heartfelt condolences to her mother and bereaved family, and my heartfelt apologies for (the) loss of this precious life in the detention centre,” Kamikawa said.
The minister said the report had not conclusively determined the cause of Sandamali’s death but found the detention centre in Nagoya in central Japan “lacked a system to assess the health of detainees and provide medical services”.
“I have instructed the chief of the immigration services agency to take control and supervise regional outlets appropriately,” Kamikawa said.
“We will carry out reforms with the determination that this never happens again.”
National broadcaster NHK said four officials at the detention centre were “reprimanded” over the death, but none were fired.
Human rights campaigners have long criticised conditions at Japanese detention centres, including how guards respond to medical emergencies.
In May, Japan’s ruling lawmakers dropped a controversial push to change rules on handling asylum seekers and deportations after opposition pressure over Sandamali’s death.
The proposed legislation included changes making it easier to deport unsuccessful asylum seekers, something that was heavily criticised by rights groups, who also say Japan should do more to take in refugees.