Uber could face the possibility of having its autonomous vehicle program shut down or slowed.

A trade secrets lawsuit filed by autonomous vehicle company Waymo may be taking a dangerous turn for ride-sharing service Uber.

The self-driving spin-off of Google has alleged that a former employee stole thousands of pages of confidential documents before leaving to set up his own company that, in turn, was sold to Uber. The case has, until now, been handled as a civil matter in U.S. District Court in San Francisco, but it could now turn into a criminal matter.

While U.S. Judge William Alsup said he would take “no position,” he did declare that there is “ample evidence” that Anthony Levandowski breached his contract when leaving Waymo several years ago, something Judge Alsup said needed to be reviewed by the U.S. Department of Justice for possible prosecution.

The civil case has been going on for weeks and centers on whether Levandowski, once the senior manager of what was then Google’s autonomous vehicle project, took 14,000 documents with him when he left the company. Levandowski went on to form Otto, a start-up focused on self-driving trucks. It was soon purchased by San Francisco-based Uber which has its own autonomous vehicle program underway.

Levandowski left Waymo to start autonomous truck company Otto, later sold to Uber.

The bitter fight could prove to be the latest in a series of setbacks for Uber. Just last week, the Justice Department began a probe of the Greyball software the ride-sharing service had developed. Uber initially claimed it was used to protect drivers from unruly customers, but critics allege Greyball also was used to keep at bay regulators who wanted to monitor Uber, notably in Portland, Oregon, where the service was not permitted to operate.

(For more on the Greyball probe, Click Here.)

Uber is also in the midst of an internal probe headed by former U.S. Attorney General Eric Holder looking into allegations of sexual discrimination within the company. It faces a lawsuit from the family of a former engineer who committed suicide due to what the suit claims was unacceptable working conditions. And Uber CEO Travis Kalanick has said he is now searching for a new company COO after he was caught on video angrily berating one of the service’s drivers.

But the Waymo lawsuit could make things significantly worse for Uber, especially as it lays out plans for the long-term future. Today, the bulk of the company’s revenues are paid out to drivers, a key reason Uber has been operating in the red. But, in the future, Kalanick wants to shift to fully driverless vehicles, arguing that this would lower the cost of an Uber ride to the point many potential customers would give up owning private automobiles.

(Sex harassment claim raises more problems for Uber. Click Here to get details.)

Uber has been working with several partners on its autonomous research program, but has said it is developing most of its capabilities in-house. Waymo’s lawsuit contends the ride-sharing service has actually been relying on trade secrets taken by Levandowski when he departed the Google spin-off.

Uber and CEO Travis Kalanick have faced a number of serious setbacks in recent months.

Uber has acknowledged that the executive did take documents when leaving Waymo, but insists it has not had access to the trade secrets nor used them to assist its own self-driving program. For its part, the Google spin-off claims the stolen material helped Uber significantly speed up its own autonomous efforts.

Uber had been hoping to push the case out of open court and into private arbitration, a move that Judge Alsup has now rejected. He has also taken a step towards granting Waymo’s request for an injunction that could bring Uber’s autonomous vehicle program to a halt.

A criminal case could seriously complicate matters for both Levandowski and for Uber. The threat of prosecution has also complicated the civil trial. The former Google employee has refused to testify before Judge Alsup, citing his Fifth Amendment rights to avoid testifying against himself. Levandowski has been concerned that any comments he might make in the civil case could then be used in a criminal trial.

But by failing to take the stand, Judge Alsup said Levandowski “has obstructed and continues to obstruct both discovery and defendants’ ability to construct a complete narrative as to the fate of Waymo’s purloined files.”

Despite the latest setbacks, Uber issued a statement saying, “We remain confident in our case and welcome the chance to talk about our independently developed technology.”

(VW CEO Mueller under investigation in latest twist to diesel emissions scandal. Click Here for the latest.)

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