It’s a bad time to shop for a new car. Car companies are spending less on discounts and incentives. The aftershocks of the disaster in Japan are making their way through the automotive supply chain, leaving some manufactures with limited inventories. And, with gas prices the highest they’ve been since 2008, fuel-efficient small cars are in high demand.

While analysts have been warning about vehicle shortages since March, it’s tough for consumers to know which models are the most impacted by supply chain disruptions. “For [car companies], there’s no upside to accepting there is a problem” with their inventories, says Jesse Toprak, vice president of industry trends and analysis at TrueCar.com. If a car company told the public that it was running short of a given model, that “might give license to dealers to charge more,” and could drive shoppers away from the brand, says Toprak. In most cases, the only way to find out if the car you want is in short supply is to rely on your dealer’s word, or try and track inventories online.

Car companies can’t hide supply problems forever, though, and analysts like Toprak track real-time sales data to assess new car inventories. If a car is selling with no discounting, analysts know that dealers are running low. If analysts stop getting transaction data on a particular model, they know it’s sold out. Right now, cars experiencing price increases that indicate a supply problem include “any model that’s made in Japan and gets good gas mileage,” Toprak says. That includes popular models like the Toyota Prius. In fact, Prius sales were down 4.3 percent in April, something that analysts say indicates a model shortage.

The Good News

If you’ve got your heart set on a car with good fuel economy, you still have options. We’ve listed cars that analysts say are in short supply and give you alternatives.

If you want a Toyota Yaris, get a Ford Fiesta.

The Toyota Yaris starts at $13,155 and gets 29/36 mpg city/highway. The Ford Fiesta starts at $13,320 and gets 29/38 mpg city/highway. Based on price and fuel economy, the two are pretty similar, except that the Yaris is built in Japan and is more dependent on Japanese suppliers than the Fiesta. Yaris supplies are dwindling, and prices are rising. The Ford Fiesta, which car reviewers like better anyway, is a great alternative to the Yaris. Bear in mind that with gas prices up, it may still be hard to get a deal on the Fiesta, but odds are, it will be better than the deal you can get on the Yaris.

If you want a Toyota Prius, get a Hyundai Sonata Hybrid.

When the earthquake hit, analysts immediately used the Toyota Prius as the poster child for supply problems. The Prius is built in Japan and is the most popular hybrid on the market. During the spike in gas prices in 2008, Toyota was left with just a seven-day supply of Prius hybrids. A 60-day supply is normal. As a result, Prius prices spiked. If you can’t find a Prius, check out the Hyundai Sonata Hybrid. It starts at $25,795, which is $2,275 more than the Prius, but comes with standard features like Bluetooth and an iPod interface. Get those features on a Prius and you’ll end up paying $1,415 more than the Sonanta hybrid. While the Sonata Hybrid can’t match the Prius’ fuel economy of 51/48 mpg city/highway, it gets a respectable EPA-estimated 35/40 mpg.

If you want a Honda Civic, get a Chevrolet Cruze.

Honda has announced that production of the 2012 Honda Civic will be reduced through the summer. At the same time, reviewers are lukewarm about the Civic compared to other small cars. In short, there’s never been a better time to check out the Civic’s often-overlooked competitors. The Chevrolet Cruze currently outranks the Honda Civic, offers a longer powertrain warranty and matches the Civic’s highway fuel economy. If you go for the Cruze’s ECO trim (which adds about $2,000 to the Cruze’s $16,525 base price) you can get 28/42 mpg, which beats the Civic’s gas mileage.

If you want an Infiniti G, get a Buick Regal.

While most cars with supply problems are fuel-efficient models, some brands have entire model lines that are built in Japan, including Infiniti. The Infiniti G is one of the brand’s best-known models because it’s a sporty and upscale sedan that comes close to the performance of the BMW 3-Series, but has a lower price. Though Infiniti and its parent company, Nissan, haven’t been as impacted by the crisis in Japan as Toyota and Honda, they are still experiencing some disruptions. An alternative to the G is the Buick Regal. The Regal starts at $5,640 less than the G and gets 19/30 mpg to the G’s 20/29 mpg. Reviewers also rate the Regal’s performance higher than the G’s.

The Bad News

While it’s great to know that you’ve got options if you’re shopping for a car right now, you still need to time the market. Toprak predicts that over the next few months prices will rise for the entire automotive industry, not just models that are in short supply. “The longer the shortages last, the greater the pricing pressure will be on the competition,” he says. “There will be a chain reaction of price increases.” 

Prices aren’t low now, but Toprak anticipates that they’re as low as they’re going to be this year. Most car companies “will not resume normal production levels until December, at the earliest,” says Toprak.  “Buy now, don’t wait. It’s not going to get any cheaper in the next six to nine months.”