NEW YORK — The nation’s car dealers have a new worry: They’re running out of vehicles.

As the “cash-for-clunkers” program reaches its next chapter, and consumers pour into showrooms, some dealers say their stock of new cars — especially for fuel-efficient smaller models — is waning.

At Larry Miller Honda in Boise, Idaho, about two-thirds of the car lot is empty. The dealership is nearly out of 2009 models — something that usually doesn’t happen until the late fall.

And the situation is so dire at a Chrysler, Dodge and Jeep dealership in Beaver Springs, Pa., that the owner, Michael Andretta, is essentially shutting down this weekend to repave his car lot.

Such a scenario amounts to a complete shift from earlier in the year, when hard-hit dealers saw cars pile up as consumers largely shunned big-ticket purchases.

It also reflects the rampant popularity of the incentive program, which gives car owners vouchers of up to $4,500 to trade in older, gas-guzzling vehicles for new, cleaner varieties.

On Friday, President Barack Obama approved another $2 billion to extend the program until Labor Day, putting consumers back in the car-buying mood. The program’s first $1 billion ran out in about a week.

However, industry officials say shoppers now searching for deals may need to be more flexible, given the dwindling number of cars on many lots. Customers hoping for a blue vehicle, for instance, may need to settle for a white one instead, said John McEleney, the chairman of the National Automobile Dealers Association.

Still, even as car lots thin, some wonder whether the new infusion of government cash into the clunkers program is actually weakening consumers’ resolve to go out and make a deal.

During the first phase of the program, which began last month, consumers flocked into dealerships, worried that they’d miss out otherwise as the money ran out. Now, shoppers may not feel as pressured.

At Crown Ford in Lynbrook, N.Y., sales manager Anthony Ciuffo said that walk-in traffic had slowed down.

“It seemed that there was more sense of urgency prior to passing the bill,” he said.