The government-funded rebate program, popular with consumers, comes to its official completion on Monday.
Dealers have until 8 p.m. to file claims for any deals.
Some dealers said they were participating in the Clunker program right up to the end. Others said they had stopped because they didn't want to risk giving a $4,500 discount on a car and not be reimbursed by the government.
AutoNation (AN, Fortune 500), the country's largest dealership chain, stopped doing Cash for Clunker transactions after Friday. AutoNation had completed over 12,000 deals, according to spokesman Mark Cannon.
"It's been a great run," Cannon said.
Under Clunkers, which launched July 27, vehicles purchased after July 1 are eligible for refund vouchers worth $3,500 to $4,500 on traded-in cars with a fuel economy rating of 18 miles per gallon or less.
Car buyers trading in a vehicle must prove that the vehicle has been titled to them for at least a year and, in most states, that the car has been insured for a year. Dealers have to provide copies of that paperwork, among other things, to the National Highway Traffic Safety Administration in order to get their rebates.
The Virginia Automobile Dealers Association reported late last week that about 25% of its member dealerships had already dropped out of the program because of uncertainty over getting paid for their deals.
The Virginia auto dealers' group reports that dealers have been reimbursed for only about 3% of all the deals that have been done in that state. Hall described the submission process as challenging, with frequent problems and rejections.
"It's been ugly, ugly," Hall said.
The principal trade group for dealers made a last-minute push to extend the deadline for dealers to submit paperwork.
In a statement released late Friday, the National Automobile Dealers Association called on the government to accept dealer rebate requests until Aug. 31. The group cited computer slowdowns that could result from "overwhelming demand" on Monday. The government has yet to rule on whether it would extend the deadline.