If you don't see a problem, get out a hose and water down the roof. Run the water down from the high point of the roof so the water travels over the area of the leak. Observe the water flow carefully, looking in areas that might look vulnerable to leaks. If that effort fails, get boots and raincoat ready and wait for a good heavy rain. Then get on the roof and carefully look around.
Nobody wants to risk life and health to crawl on their church roof in the middle of a hard rain.
But it could very well reveal the problem. You probably should hire a reputable roofing contractor to do this for you and to make the repair. I have long opposed building a church with a basement. Not only are they a constant threat for leaks, but they usually are not very livable spaces. Not building a basement is the best way to prevent a leaky basement.