The Transportation Department along with NASA engineers said two mechanical defects previously identified by the government - sticking accelerator pedals and gas pedals that can become trapped in floor mats - are the only known causes for the reports of runaway Toyotas.
Both issues were the subject of large recalls by Toyota - more than 12 million Toyota vehicles worldwide have been recalled since 2009 as a result of those issues.
Transportation Secretary Ray LaHood said the department's 10-month investigation has concluded there is no electronic-based cause of unintended high-speed acceleration in Toyotas.
"We feel that Toyota vehicles are safe to drive," said LaHood during a Tuesday press conference.
The recalls have posed a major challenge for the world's No. 1 automaker, which has scrambled to protect its reputation for safety and reliability.
Toyota's safety issues received broad attention from the government after four people were killed in a high-speed crash involving a Lexus near San Diego in August 2009.
The National Highway Traffic Safety Administration has received about 3,000 reports of sudden acceleration incidents involving Toyota vehicles during the past decade, including allegations of 93 deaths. NHTSA, however, has confirmed just five of them.
NHTSA officials said they reviewed consumer complaints and warranty data and found that many of the complaints involved cases where the vehicle accelerated after it was stationary or at very low speeds.
Upon investigation, officials said that in many cases when a driver complained that the brakes were ineffective, the most likely cause was the driver stepping on the accelerator instead of the brakes.
The Transportation Department enlisted the help of NASA for the study primarily for their expertise in electromagnetic interference and software integrity.
LaHood said NASA engineers rigorously examined nine Toyotas driven by consumers who complained of unintended acceleration - looking at hundreds of thousands of lines of software code and testing mechanical components that could lead to sudden acceleration.
A preliminary part of the study, released last August, failed to find any electronic flaws based on a review of event data recorders or vehicle black boxes.
Many newer vehicles use electronic throttle control with sensors and computer chips that pass commands between the accelerator and the engine, and some safety advocates claim the systems are prone to malfunction.
Despite the negative spotlight Toyota was under during the recall, they've managed to see decent sales numbers. The company said they have raised their full-year net profit forecast for its business year which ends in March.
After the results of the government investigation were revealed, shares of the automaker climbed on the New York Stock Exchange following the news. Toyota shares were up more than 4 percent, to 89.00 in mid-afternoon trading.
Despite its findings, LaHood said the National Highway Traffic Safety Administration was considering new regulations to improve safety. They include requiring brake override systems on all vehicles, standardizing keyless ignition systems and requiring event data recorders, or vehicle black boxes, on all new vehicles.
The Associated Press contributed to this report.