I have a new 2011 Prius 3. (1900 miles)The other day I had my elderly mother waiting in the car for me while I got her some groceries. When I returned the interior smelled like exhaust. (she didn't notice). The ac was off but set to outside air with the fan running. I figured it was because I was parked and maybe sucked in exhaust from another vehicle. However last night I noticed the odor again this time just from regular driving with the ac set to outside air and I could smell it again. I checked the oil filler cap as suggested in a previous post. I smell it more on my clothes when I leave the car than when I'm driving it. weird.
If you are sure it is not sucking in exhaust from other vehicles it would be best to take it to the dealer and try to convince them you have a problem. If it's obvious and they can smell it too, no problem. But if it isn't obvious to them and you can notice it because you have a sensitive nose you may have to find someone else who can smell it also. This is a first on this site, as far as I know, for this particular problem. That doesn't mean it's not real, just that it's unusual. Before you take it in make sure the hatchback is shut and the rear windows up when you smell it. Could be getting in that way. Good luck and be sure to keep us posted.
After removing many of the inside panels in the rear, I can see where exhaust could enter the cab. With that said, with the fan on, you should have positive pressure inside eliminating that problem. Do you have a portable CO detector? Might be one way of proving it.