Uber's court battle with Alphabet's Waymo isn't going well for the ride-hailing startup.

A federal judge on Thursday referred Waymo's theft allegations to the U.S. Attorney's office for investigation. The judge, William Alsup, said he wasn't taking a position on whether a prosecution is warranted.

It's the latest in a series of setbacks for the embattled company.

Waymo, formerly Google's "self-driving car" company, is suing Uber over technology it says was stolen by former Waymo employee Anthony Levandowski.

Levandowski left Waymo in January 2016 to start autonomous truck company Otto, which Uber bought for $680 million in August 2016. Waymo claims he absconded with 14,000 top secret documents, an allegation that Alsup has said is not in question.

Uber and Waymo both declined to comment on the referral of the case to the U.S. Attorney's office.

Related: Uber and Waymo face off in court over stolen self-driving tech

The judge also ruled on Waymo's request to put a halt on Uber's research and development in self-driving technology until the case is settled. He ordered a partial injunction, but the court document remains under seal, making it unclear to what degree Uber's self-driving program will be affected.

In a contentious hearing last week, Levandowski refused to answer questions during his deposition, taking the fifth amendment.

On Thursday, Alsup said Levandowski's stonewalling has "obstructed" the case.

Related: Uber's top self-driving exec steps aside amid lawsuit

In another blow, the judge denied Uber's request to move the case out of the courts and into arbitration. Waymo's suing Uber in court "was not only reasonable but also the only course available," he wrote.

Uber called the denial of arbitration unfortunate, saying in a statement: "We remain confident in our case and welcome the chance to talk about our independently developed technology in any forum."

Waymo celebrated the judge's decision, calling Uber's request to move the case to a private legal forum a desperate bid.

"We look forward to holding Uber responsible in court for its misconduct," Waymo said in a statement.

-- Keith Allen, Heather Kelly and Jethro Mullen contributed to this report.