The Tokyo dealership chain called Toyopet is expecting eight more Prius cars to be brought in for reprogramming later in the day. Owners are being asked to wait about 40 minutes.
Makiko Noguchi, a 61-year-old producer for a video company, was sipping tea in the showroom, anxiously waiting for her Prius to get fixed.
"I never experienced any problems," she said. "If anything, I'm more worried about what they're doing to my car now."
Like many other Prius owners, she was mystified by Toyota's handling of the recall. All Toyota needed to do was come out with an explanation sooner, she said.
It wasn't until Tuesday that Toyota announced the global Prius recall. The company acknowledged last week it had quietly fixed the glitch in cars in production from last month - a disclosure that did little to assuage growing consumer doubts.
The recall for the Prius, the world's best-selling hybrid, comes on top of more than 8 million Toyota vehicles recalled in the last four months outside Japan for problems with floor mats that can entangle gas pedals and a defective gas pedal.
Toyota, which built its reputation on near-perfect quality, has been widely criticized as too slow and irresponsible in managing its recall crisis.
The scrutiny of Toyota's possible mishandling of the problems will move to Congress in coming weeks, with hearings in the House and the Senate to see if all the causes of Toyota's acceleration problems have been identified.
Toyota says the latest problem with the Prius produces a sensation that the brake power is weakening. That happens only on slippery or bumpy surfaces when antilock brakes kick in. If the driver steps heavily on the brake pedal, the car will stop.