The report had threatened to overshadow Toyota's attempts to restart sales after a punishing series of recalls.
National Highway Traffic Safety Administration engineers drove the hybrid in an effort to recreate the episode reported by the driver, James Sikes, but were unable to do so, the agency said in its first statement on a hurried and high-profile analysis.
"We would caution people that our work continues and that we may never know exactly what happened with this car," NHTSA said.
Sikes, 61, had reported in a call to emergency telephone operators that his Prius was racing out of control for some 20 minutes before he could slow down the vehicle and bring it to a safe stop with coaching from a California Highway Patrol officer who pulled alongside him.
But Toyota said it had found no evidence that Sikes had been applying the brake forcefully as he had claimed and said he should have been able to stop the Prius by doing so, or by shifting into neutral or turning off the electronic power switch.
The March 8 incident came at a crucial time for Toyota.The automaker has been struggling for almost two months to reassure a jittery public it has turned a corner in dealing with safety issues that sparked a recall of 8.5 million vehicles worldwide.
Although Toyota's March U.S. sales have been up sharply because of cash rebates and zero-percent financing offers, some analysts have said the long-term commercial damage from the automaker's safety crisis remains harder to assess.
Scrutiny of the Prius, a vehicle the automaker considers its most important, has also raised the stakes for the automaker in ongoing U.S. regulatory and congressional investigations of unintended acceleration.
Toyota plans to cut output of the Prius by 10 percent starting this month due to a sales slowdown, a source with knowledge of the plans told Reuters.The 2010 Prius was the subject of a February recall for braking problems, and the 2004 to 2009 model-year Prius hybrids were included in an October recall for loose floor mats.
But the San Diego case was the first to trigger a federal examination of the Prius for unintended acceleration, something U.S. consumers have complained about in a range of other Toyota models, including its top-selling Camry.
California police have said they had no reason to doubt Sikes based on the burning brakes in his car and observations of the officer who helped him.
Toyota, which convened a news conference in San Diego to question Sikes' account of events, declined to comment directly on whether Sikes might have misled investigators.
But Toyota said an examination of his Prius showed that the car was being driven with the brakes lightly and repeatedly applied -- some 250 times over the period of the incident.
The brake override in the Prius would have cut engine power to the vehicle had the driver applied "moderate to heavy" pressure on the brake pedal as Sikes had claimed, it said.
Sikes could not be reached for comment. The San Diego-based law firm representing him said it would not comment until NHTSA had completed its investigation.
Toyota has said it has not been able to identify a cause for cases of unintended acceleration consumers have reported beyond ill-fitting floor mats and sticky accelerator pedals. The automaker has recalled more than 6 million vehicles in the United States for that pair of problems since October.
Commentators have focused on the prospect that drivers could be making mistakes -- hitting the accelerator instead of the brake -- or that Toyota vehicles could be subject to a software glitch or other problem that is hard to replicate.
Toyota said again on Monday that there is no evidence for that latter possibility -- a hypothesis that some critics have dubbed "the ghost in the machine."
"The hunt for the ghost seems to ignore or fly in the face of known facts," Toyota spokesman Mike Michels said outside a San Diego sports stadium where the automaker demonstrated the safety systems on the Prius for reporters."There's no evidence that the system heals itself mysteriously," Michels said.
Kelley Blue Book analyst James Bell said Toyota needed to do more than discredit one report of unintended acceleration to reassure consumers. "Until they have a more definitive answer, the elephant stays in the room," Bell said in an email.
A Santa Barbara, Calif-based firm that tracks vehicle resale values, said Toyota's recalls had damaged the brand. It said its survey of consumer attitudes showed Toyota had dropped to No. 6 from No. 1 in perceived quality.
In response to weaker demand, Toyota will probably need to extend aggressive discounts through June, ALG said.
Sikes had told police and reporters he was driving the car on a freeway when it unexpectedly surged forward and reached speeds exceeding 90 miles per hour.
Two NHTSA investigators joined Toyota experts to examine his Prius, including an on-board diagnostic system designed to record information about the car's various systems.NHTSA has been criticized by Congress for not aggressively investigating complaints against Toyota.
Authorities believe floor mat problems in Toyota and Lexus vehicles are linked to five U.S. crash deaths since 2007. Another 47 crash fatalities reports over the past decade have been reported due to unintended acceleration in Toyota vehicles, according to NHTSA.
There are 59 reports of fatalities linked to episodes of unintended acceleration for other automakers over the same period, NHTSA says.