Still an interesting article, since it reveals that the Japanese take their secrecy really, really seriously, and so we may not assume much of what they are up to, really.
The problem with secret government agencies is otherwise generally that they are notoriously difficult to reign in. They are governed by law, but are likely to develop their own agendas, and since lawmakers are kept in the dark they can end up meddling in policy, using all the means at their disposal.
Our ultimate line of defense against such, and only hope are the brave whistleblowers. Edward Snowden needs to be pardoned.