Codes have a letter in front of them, typically P, so I found this code strange. Fortunately Adobe Reader can find the codes by only the number.
However, I only have the repair manual for 2004, which would also work for 2005, and mostly work for 2006 (the drivetrain is the same, but much of the 'entertainment' electronics have changed).
For the new generation, P3009 indeed indicates a short in the high voltage, and there would be a sub number (INF code) that would narrow down the source. I doubt it is the battery itself that is triggering the code, and I think you would have worse problems than you describe if a short were the problem. The high voltage system is floating from ground, so either side touching ground either directly or through a high resistance could trigger this error. It is not likely though in normal use of the car that you would come across both sides of a circuit completing a dangerous path through you. Did you know that you often touch one end of your household wiring on a regular basis? But depending on the nature of the leak, the system may allow normal driving, or may go into limited driving mode. For the new Prius, even putting the wrong AC compressor oil can trigger this code.
You say the dealer didn't transpose the number, did he show you the display on the scanner showing the error coming from the car? If not, he may have transposed digits.
It's too bad you didn't press the issue while it was still under warranty if this indeed was the code.
By the way, you can go to many auto parts store chains, and even some repair centers and they can extract codes free of charge or for a very small fee. They may not be able to interpret the code, but they can give you the numbers and then we can research it for you.