What do you mean not permitted? That the house was built in an area where no homes are allowed? Tthat the house was built with out permits to build ? That the house was built in an area not zoned for homes? THat the house was not built to code conformance?
I cannot believe you would be able to close on a home that was not "permitted" in any way, shape or form. Given the amount of inspections, paperwork involved during the process SOMEONE had to know there might be a problem.
Anyway, without much information the best advise anyone can give you is to speak to an attorney to straighten this out.