Steve is right. You should rebuild the roof with a slope.
I bought a house with a flat roof section, and of course it leaked. Unfortunately it had leaked for a while so some of the structure was rotten. I tore off the roof, replaced the rotted structure, rebuilt a sloped roof and everything is fine.
If you don't have rot now, you will later. Attack the problem head on by building a sloped roof and prevent later costly repairs.