The rationale behind the charge appears to be the Ministry’s desire to control "illegal" "radio stations" and to promote "efficient" RF spectrum utilization. Japanese consumers already pay a yearly 420 Yen fee for each mobile phone.
The Ministry opened a public comment phase, which closes on next Thursday, July 19.
While the proposed fee is for Japan only, there is obvious industry concern about the establishment of a precedent that could be followed by other countries.
References to the proposal (in Japanese) and related documents can be found at the following links:
July 5 pre-meeting
July 5 meeting report
Background for the wave utilization charge system