The indictment filed on Tuesday by the US Attorney’s office in San Jose, California, is an offshoot of a lawsuit filed in 2017 by Waymo, a self-driving car pioneer spun off from Google.
Uber agreed to pay Waymo 245 million US dollars (£199.38 million) to settle the case.
But the federal judge overseeing the lawsuit made an unusual recommendation to open a criminal probe after seeing enough evidence to conclude a theft may have occurred.
Uber considered having self-driving technology crucial to survive and counter potential competitive threats from Waymo and dozens of other companies working on robotic vehicles.
It wants to build self-driving cars so it can eliminate the need to have a human behind the wheel, one of the biggest expenses in its ride-hailing service.
Anthony Levandowski, a pioneer in robotic vehicles, was charged with 33 counts of trade secrets theft.
Each count carries a penalty of up to 10 years in prison and a $250,000 (£203,451) fine, or $8.25 million (£6.71 million) if convicted of all counts.
Miles Ehrlich, one of Levandowski’s attorneys, maintained his innocence in a statement read outside the courthouse.
“He didn’t steal anything, from anyone,” Mr Ehrlich said.
“This case rehashes claims already discredited in a civil case that settled more than a year.”
Prosecutors said the probe is ongoing but they would not disclose whether Uber and its founding CEO Travis Kalanick are targets.
Google and Uber co-operated in the investigation, they said.
Although Tuesday’s indictment did not charge Uber, it is a stain for a company that has been trying to recover from a series of scandals since jettisoning Mr Kalanick two years ago.
The case seems unlikely to endear Uber with investors already sceptical about the company’s ability to make money after piling up billions of dollars of losses.
The lack of profits is the main reason the company’s stock has fallen about 25% below the price set during its initial public offering of stock in May. Nonetheless, Uber’s stock fell less than 1% after the announcement.
The FBI depicted its pursuit of the complex case as a sign of its commitment to protecting technology considered vital to the economy’s growth.
“Silicon Valley is not the Wild West,” said John Bennett, the FBI agent in charge of the investigation.
Prosecutors said Levandowski turned himself in earlier on Tuesday.
During the Waymo trial, Mr Kalanick conceded Uber needed to develop self-driving cars to survive.
He denied he ever resorted to stealing technology from Google, which he believed was an ally until he began to suspect the company intended to launch its own ride-hailing service consisting entirely of its robotic vehicles.
Mr Kalanick also testified his push to build a fleet of self-driving cars for Uber led him to woo Levandowski, who at the time was considered to be a pioneer in robotic vehicles.
Levandowski left early the following year to devote his time to Otto, a self-driving truck company he started with another Google employee, Lior Ron, who also left.
Uber bought Otto later in 2016 for $680 million (£553.38 million).
Waymo, which spun off from Google in 2016, alleged Levandowski downloaded 14,000 documents containing its trade secrets before he left for Otto.
Uber denied knowing anything about those documents but eventually fired him after he repeatedly asserted his constitutional right against self-incrimination leading up to the trial.
Mr Ehrlich’s statement on Tuesday said Levandowski downloaded the documents as an authorised Google employee and never brought those files to Uber or any other company.
A former Uber security specialist, Richard Jacobs, claimed the company employed an espionage team to spy on Waymo and other rivals while creating ways to conceal any stolen technology.
Google also pursued a separate case against Levandowski in arbitration proceedings, which resulted in a panel ordering Levandowski to pay the company $127 million (£103.36 million), according to disclosure made by Uber leading up to its IPO.
Uber may be held liable for paying all or part of that as part of guarantees it made in its Otto acquisition but believes it may be able to get out of those obligations.
After Levandowski left Uber, he started another self-driving start-up called Pronto, which said on Tuesday he would no longer be its CEO as he defends himself against the charges.