U.S. district judge William Alsup also partially granted Waymo's bid for an injunction against Uber's self-driving efforts, and rejected Uber's arguments that the trade secret allegations should proceed in private.
Google's self-driving Waymo car division originally filed the lawsuit against Uber in February, accusing the company of stealing its self-driving intellectual property.
Specifically, former Google employee Anthony Levandowski is accused of stealing 14,000 confidential files that included data on Waymo's laser-based radar (LiDAR) system, which the company called "one of the most powerful parts" of its self-driving technology.
In referring the case to the U.S. Department of Justice, Judge Alsup said that in the absence of "smoking gun" proof of wrongdoing by Uber, he was not taking a position on whether or not charges are warranted, but noted there was "ample evidence" that Levandowski had breached his duty of loyalty to Waymo.
Uber declined to comment on the referral to prosecutors, while Levandowski has already recused himself from LiDAR-related work while the case is ongoing, but the news is yet another setback for the ride-hailing service as it attempts to revive its tarnished image following multiple controversies over recent months.
The Department of Justice is already investigating the company over its use of "secret" software that allowed its drivers to operate in areas where Uber was banned or restricted. The so-called "greyball" software is said to have allowed the company to identify undercover officials and block them from booking rides, in order to prevent them from proving that Uber was operating illegally.
Last month it emerged that Apple CEO Tim Cook threatened to pull Uber's app from the App Store in early 2015 after discovering that it was secretly "fingerprinting" iPhones that used the app. Uber said it used the identification method to prevent fraud, despite knowing the tactic is a clear violation of Apple's app privacy guidelines.