It really depends. If there is no line and you know how to fill out the forms, it will take 3 minutes at most. The norm, however, is 20-30 minutes because there are several people in line, you didn't fill out the form correctly and was sent back to write up a new one, the more stringent clerks takes their time copying the ID info down (or in the most extreme cases wants to make a photocopy of the passport), etc.

Considering the OP for this particular discussion doesn't want even waste a minute sweating out the transfer from NRT to HND, it's best that he just CC the bus ticket. Exchange rate will probably be better anyway, even considering the international transaction fee Visa/MC will slap on.