On one hand the journalist's account in the Economist has many places that sound fishy. On the other hand, abuses in such facilities in Japan is a known issue repeatedly
reported by the Amnesty International. There are even unlucky souls who have been suffering prolonged psychological issues after release or even died during their stay.
If you can read Japanese, you may search for 上陸防止施設 and 入管収容施設. There are accounts by Japanese who worked in those facilities on the gravity of the abuses there.
Here is a good discussion on this particular incident:
http://www.hikosaemon.com/2012/01/ja...migration.html