I had the same problem with my Ford Escort Wagon, and I had the window seals tested for leaks by Speedy Auto Glass; results, negative. Stymied, I put newspaper along the sides of the trunk area and finally found the culprit: a damaged seal on the side marker light. You may have a similar problem with your Prius. If you take out the storage bin and the cargo deck that covers it, then carefully lay a sheet of newspaper across the opening, you should be able to track where the water might be coming in from.
Because the tire well is the lowest point in the car, the water might not necessarily be coming from the rear end of the car but could be trickling along the sides, possibly from a leaky door seal.
The proximity to the high voltage battery would make it imperative that you eventually locate the source and stop the leak, as I am sure you are doing.
On a really dry day, you can still use the newspaper trick; move the source of water (garden hose) around the car and starting with the lowest possible point of entry, the bottoms of the doors, until you find water coming into the car.
Next to electrical problems, leaks are the most maddening. This should be covered under warranty.
Good luck,
Bob