Anthony Levandowski was charged with 33 counts of trade theft involving Alphabet’s self-driving car technology.
He had left Alphabet’s Waymo unit in 2016 and eventually ran Uber’s self-driving car project, only to be fired.
The 39-year-old, who now runs his own firm, denies the charges.
“Not a single one of these supposedly secret files ever went to Uber or to any other company or person,” said Miles Ehrlich, a lawyer for Mr Levandowski.
Waymo and Uber were involved in a protracted lawsuit, which the taxi company eventually settled in 2018. Mr Levandowski was not party to that case, and did not publicly comment on the allegations.
The claim is that before leaving Waymo, Mr Levandowski downloaded thousands of files in 2015 related to Alphabet’s self-driving car technology, including details related to Lidar, a crucial sensor technology for self-driving cars.
“All of us have the right to change jobs, none of us has the right to fill our pockets on the way out the door,” Californian federal prosecutor David Anderson said. “Theft is not innovation.”
In the 2018 settlement, which underlined technology companies’ race to lead the market in autonomous technology, Uber promised not to use Alphabet’s technology and to give Waymo a 0.34% stake in Uber.
Mr Levandowski faces up to 10 years in jail and could be fined $250,000 per count, $8.25m in total.
He was a founding member of the group that started Google’s self-driving car project. Mr Levandowski left Google in early 2016 to launch his own self-driving software start-up called Otto, which was later acquired by Uber.
Uber said it had “co-operated with the government throughout their [DoJ] investigation and will continue to do so”.