Bathroom Exhaust Water Penetration

Flat roof. Bathroom exhaust on second floor (top level) experiences water penetration during really bad storms, but not always. Water drips through the exhaust fan leading to water stains on ceiling. Looking at it from the roof, the cover on the exhaust seems to be in order. We had a new roof put on est. 5 years ago and it looks to be sealed well. Obviously it cannot account for “sideways” rain gusts. Exhaust cover is mounted at a flat 90 degrees. Any tips here?