The secretary is safe and was not in any danger, a Pentagon spokesman told Fox News -- though one coalition service member was injured.
According to spokesman Capt. John Kirby, an unidentified Afghan was driving an apparently stolen pickup truck at high speed toward the ramp where Panetta was supposed to land at Camp Bastion in Helmand Province on Wednesday.
But the vehicle ran into a ditch and caught fire right before the landing -- Panetta's flight was switched to land at a different ramp on the same base at the last moment.
Before crashing, the driver hit and injured a coalition service member with the truck. The Afghan driver was also burned over most his body and is now in a military hospital. No explosives were found.
"We have no confirmation that this speeding vehicle posed a threat to the secretary's health. At no point was the secretary's safety in jeopardy," Kirby said.
Pentagon spokesman George Little said there was no indication the incident was anything other than a stolen vehicle. However, the motive and the individual are under investigation.
The incident comes as tensions run high in Afghanistan. A U.S. soldier is accused of going on a shooting spree several days ago that left 16 Afghan civilians dead. Afghans have also been protesting over the inadvertent burning of Korans at a U.S. base.
The International Security Assistance Force said in a brief statement Wednesday that the incident at Camp Bastion did not put Panetta or any of those on the aircraft in "any danger."
The statement said the driver is now in custody, and an investigation is underway.
Fox News' Jennifer Griffin and Justin Fishel contributed to this report.