"It is not part of the Toyota culture and Toyota way to cover up anything," said Yukitoshi Funo, one of Toyota's five executive vice-presidents at its Tokyo headquarters.
The Toyota denial comes after U.S. highway safety officials rebuked the company for falsely claiming government inspectors had found "no defects exist" in the suspect cars other than loose floor mats.
Toyota has recalled some 3.8 million floor mats and had said that should fix the problem.
"This matter is not closed," said a statement issued by the Department of Transportation and the National Highway Traffic Safety Administration (NHTSA).
"Removal of the floor mats is simply an interim measure, not a remedy of the underlying defect in the vehicles," the U.S. statement said.
A growing number of Toyota owners say their car experienced acceleration surges of up to 100 miles per hour even though their cars did not have the recalled floor mats or, in some cases, any floor mats at all.
Some owners suspect a glitch in the Toyota computer that controls acceleration.
"No manufacturer is going to come out and say 'we've got an electronic problem and by the way, we don't have a fix for it yet,'" said safety analyst Sean Kane, who works with government regulators, plaintiffs' lawyers and auto companies.
While the focus of the federal investigation relates to Toyota floor and gas pedal design, the Toyota executive said today that a broad range of possible causes is also being discussed.
"Certainly we are talking about floor mats, but at the same time, the vehicle side too," said Funo in response to a question about an electrical problem.
Click here to hear all of Funo's comments, while speaking with reporters at Toyota's Tokyo headquarters.
Federal inspectors said they were unable to find any computer or electronic defect in six separate investigations since 2003, but added it "does not constitute a finding by NHTSA that a safety-related defect does not exist."