Kumamoto Prison in the city of Kumamoto was housing 110 earthquake survivors in part of its facility as of Tuesday morning.
It is the first case anywhere in the nation of a prison acting on a plan to open its doors to disaster evacuees.
Because the facility has sufficient food reserves and independent supplies of water and electricity, it is now lending a hand, the Justice Ministry said.
"This is the first time for a prison to be officially accepting evacuees as a part of regional contribution," a ministry spokesman said.
In the aftermath of the Great Hanshin Earthquake in 1995, some people evacuated to a juvenile detention center, but it was an ad-hoc emergency measure for which no prior plan had existed, the spokesman said.
He explained that the martial arts dojo used by Kumamoto Prison staff was opened to the public Friday night, following the first major quake the evening before.
Relatively few people used the facility that first night, but many local people have rushed in since the second major quake struck early Saturday, hitting a high of roughly 250 evacuees, the maximum allowed.
Prison staff from Fukuoka, Yamaguchi and Hiroshima prefectures joined in to provide help.
Cracks in the walls and a fallen fluorescent light bulb in the prison workshop have been confirmed, but there are no reports of confusion among the prisoners or injuries of any kind.
As prisons do not fall under the Disaster Relief Act, Kumamoto Prison would receive no new rations in an emergency. Therefore, it keeps a large stockpile of supplies.
The facility has no shortage of water or electricity because it has a well and is equipped with a backup power generator. Some people have come from great distances to get water, having learned about the well on social media posts.
After the Great East Japan Earthquake in 2011, agreements were made between local governments and prisons and juvenile detention centers, including Kumamoto Prison, to use such facilities as evacuation centers in times of emergency.
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