The move mirrors the change in authority for issuing foreign residence cards from the local municipalities (ward offices) to the Justice Ministry (MOJ).
Special permanent residents of Korean origin (zainichi) will be exempt from the changes, but foreign nationals residing in Japan under medium- to long-term residence status will need to change from the old alien registration card, first introduced in 1947, to the new cards with an embedded IC chip in them.
Foreigners can apply for the new cards at their nearest regional immigration office from January 13, 2012, though the present alien registration card remain valid for 3 years when they will be replaced by the new card. Check the front of your gaijin card where it says in red: "Renew within 30 days starting from." to see how long it is still valid.
Permanent residents will have to apply for the new residence cards within 3 years from July 2012. According to the Japan Times newspaper, "Required materials necessary for an application have not been determined yet," which sounds rather ominous.
Information stored on the chip will include the type of visa of the card holder and work and home addresses. The fine of 200,000 yen for failure to carry the new card remains the same as the old alien registration card.
As a sweetener to yet more controls on foreigners entering or residing in Japan in addition to mandatory electronic fingerprinting on arrival, the maximum period of stay for some types of visa will be increased from 3 to 5 years and re-entry permits (aka "gaijin tax") will be abolished as long as the period outside Japan is less than one year.
New arrivals on medium and long-term Japan entry visas will receive an application form for the new card. Other changes afoot from the MOJ include "the issuance of a Special permanent Resident Certificate."
Akihiro Yamaguchi, a spokesman for the Japanese Ministry of Justice added, "Foreigners are a potential threat to a homogeneous society such as Japan and need to be strictly monitored and controlled through finger printing and IC chips to protect and reassure the Japanese people." I made the last bit up, but that could be interpreted to be the message the foreign community in Japan is hearing.
However, the MOJ in its Basic Plan for Immigration Control (4th Edition) argues that as the government is actively promoting immigration to counter population decline ("In the future, Japan intends to actively promote the acceptance of foreign nationals") and also encouraging overseas students to study in Japan to reach the government target of 300,000 foreign students, more efficient and centralized means of immigration control are required as these foreigners begin to settle in Japan. Hence the need for the new cards.
For further information see the pdf document Basic Plan for Immigration Control (4th Edition) provisional translation from the MOJ website.