I don't know what, "I want to build this web application at no cost from the ministry" means but as for charging users per transaction, I believe you can use Interswitch for that. From what I hear though, you need like N150K as a deposit to open an account with them (if I am wrong, I stand corrected).
As for how to present in proposal, you could say something like, "it is the intent of xyz company to put these services online so as to reduce, if not totally eliminate, overhead associated with applying for such services by hand/costs associated with hiring pple to do it. In the end, these online services will make for a very efficient process" or something like that.
With respect to the last part of the paragraph above, you might have a problem with your local civil servants union in which case, you would be strictly OYO, but hey, that's the price to pay
