It would be for immigration as that is the only thing under the Justice Ministry's control (customs is a different ministry and security is private).

The Sankei version of the article explains that you would first have to come to Japan and register for the system at an airport here, after which you would be clear to use (what appear to be) the existing automated gates, currently only available to Japanese citizens and residents. However the system would be initially limited to business travelers, so you technically couldn't use it as a tourist or other frequent visitor.