I'd also mention that in my experience applying for this at Narita seemed to be more successful than at Haneda.

I initially tried at Haneda but my fingerprints were too weak to be picked up. The guys there just shrugged their shoulders and said sorry..can't help you. Then I tried again at Narita and there's a lady there who has been doing this for like 8 years and knows a bunch of tricks to get it to work. I eventually got registered after much persistence and I've since never had any issue using these gates.