Belmont-San Carlos Fire Marshal Jim Palisi told the San Mateo County Times the Nov. 9 fire began in Young's 1959 Lincoln Continental and spread to the nearby warehouse in the San Francisco Bay area.
Young had converted the car to run on batteries and a biodiesel-powered generator as part of his LincVolt project to create the world's most efficient full-size vehicle.
Young had just returned from Las Vegas where LincVolt was presented at the SEMA automotive show.
In a message posted on the LincVolt website, Young wrote, "Lincvolt was severely damaged in the fire. We are still investigating the exact cause although it appears to be an operator error that occurred in an untested part of the charging system.
"We do know that the car has been operating perfectly for almost 2 thousand miles and the system in question would not be in use while driving the car. We are investigating the components involved with plug-in charging."
He also said a computer in the car which may function as a "black box" may offer information about the fire.
"While this is a setback for us we are planning ways to continue. We will begin cleaning and inspecting Lincvolt today," he said.
LincVolt, which weighs 2.5 tons, is 19 feet long, can go 160 mph, and has zero admissions, was featured in a December 2008 video report by CBS News correspondent Hari Sreenivasan about car re-designer Johnathan Goodwin and his "green" music cars.
About $1 million in damage was caused by the two-alarm blaze at the 10,000-square-foot building - three-quarters of that to the contents, which included memorabilia stored there by Young and his family.
Young thanked the Belmont-San Carlos Fire Dept for an "exemplary job," and for protecting a lot of archival items which were threatened.
Fire crews were able to save about 70 percent of the warehouse's contents, including other cars and music equipment belonging to Young.
No one was injured in the fire.
Young lives nearby in the unincorporated San Mateo County community of La Honda.