The investigation covers the 2010 model year Prius.
Meanwhile, the Nikkei
newspaper reported that Toyota would recall an estimated 270,000 units of Prius in the United States and Japan to fix the brake problem.
Mike Michels, a Toyota spokesman, said he could not comment on that report. He said the car maker had no plans to suspend sales of the Prius as it did with eight other models recalled for a faulty accelerator pedal.
"There is no plan for suspension," Michels said.
"No confirmation of a recall for US at this time," he said in an email to Reuters in response to a question about the Nikkei report.
NHTSA also refused to comment on the report and said that any recall would be announced by Toyota.
Toyota changed the software controlling braking in the Prius on models manufactured in Japan from last month, a step it had not announced before Thursday.
Dennis Virag, president of Automotive Consulting in Ann Arbor, Michigan, said Toyota's revelation that it had been aware of the Prius problems for months and had worked out a quiet fix on the assembly line without notifying consumers was "shocking."
"It could be a kiss of death," he said.
Its shares dropped another 2 per cent in New York on Thursday. The stock has lost 20 per cent since it announced a sweeping recall for accelerator problems in late January.
Toyota expects costs and lost sales from its massive safety recall to total $2bn by the end of March.
The car maker's US sales tumbled 16 per cent in January and are expected to fall further in February.
The 2010 model Prius is a completely redesigned version of the iconic hybrid that Toyota has said is the most important vehicle in its line-up and almost a brand on its own.
|Toyota expects lost sales from massive safety recalls to total $2bn by the end of March [AFP]
Toyota sold almost 140,000 Prius hybrids in the United States in 2009. That represented almost half of all hybrid sales in the market.
Like other hybrids, the Prius captures the energy from braking to recharge an on-board battery to boost mileage from its gasoline engine.
Toyota Managing Officer Hiroyuki Yokoyama, who oversees quality, said Toyota had reworked a software programme that controls the interaction between the "regenerative" braking and the friction braking systems.
On bumpy roads and on ice, the regenerative brakes appear to slip, allowing the vehicle to lurch forward before the traditional brakes engage, Prius owners have said.