A year ago, the Toyota Prius was a smoking-hot commodity due to record-high gas prices. In fact, used Priuses were selling for more than new models cost because dealers simply couldn’t keep the new models on their lots.

Now it appears as if Cash for Clunkers has led to another Prius shortage and subsequent price markup.

Affordable, fuel-efficient cars like the Toyota Corolla and Ford Focus got a lot of media attention while they occupied the program’s top-sellers’ spots, and the Prius was flying off dealership lots, too. Once again, inventory ran low, which led some dealerships to add a market value adjustment (in other words, a price increase) of up to $5,000.

We also reported earlier that Toyota is having trouble making enough battery packs for its legendary hybrid, which is slowing production. This could also factor in the Prius-shortage.

With the Clunkers program over, though, and a little diligent searching on the part of consumers, buyers in the market for a Prius should be able to find one. Meanwhile, the market for highly efficient hybrids remains Toyota’s domain thanks to the Prius.

Exclusive: Rogue Toyota Dealers Price Gouging on Scarce 2010 Prius’s (Daily Tech via Autoblog)