The government encourages smaller churches to be nondescript, as in out of sight and out of mind. The bigger ones are showpieces as examples of Malaysian diversity. That doesn't prevent simple shop lots of being raided and inspected just in case they are being used for religious reasons. I've seen a letter from the local council certifying a thorough inspection had been done being framed in a shop because the owner was fed up of being accused using the premises as an illegal church.

Tell me about it, I've helped a church to do the necessary paperwork for the land usage conversion and it took nearly 10 years.