The place is called RegTP, which stands for something like Regulation Authority for Telecommunications and Postal services.
The is a special department for ship's stations called Seefunk.
I have not found this sector in English on their website, the German language URL is: http://www.regtp.de/reg_tele/start/fs_05.html
I found them very friendly and responsive, it took only a week from sending in an application to getting back a ship's station license.
The form for filing are online. The only snag is, that you need a technical approval number for the devices you are registering. I'm not sure if these numbers are Europe wide or Germany specific. Sometimes the approved models are slightly differnt, say from units sold for example in the US.