According to the Associated Press, the company was told to take its self-driving cars off the roads until it obtains the permit needed for testing autonomous vehicles on public roads.
The California Department of Motor Vehicles said Uber was expected to secure such a permit but the company claimed it did not need this clearance as a driver was also present in its autonomous vehicles that were on the roads.
Uber has been running such trials in Pittsburgh and the San Francisco trial is an extension of the programme.
The report of Uber autonomous vehicles going through red lights was published in the San Francisco Examiner.
The newspaper published video that showed a self-driving car going through a red light at the same time as a pedestrian was attempting to use the zebra crossing to cross the road.
The video was from a taxi company known as Luxor. Charles Rotter, operations manager at Luxor, confirmed to the Examiner that the video was from Wednesday.
"Yes, the dashcam of one of our ramp vans at 10:37 this am," he wrote, in an email.
The Examiner also quoted a tweet from a freelance writer saying: "Just passed a 'self-driving' Uber that lurched into the intersection on Van Ness [Avenue], on a red, nearly hitting my Lyft."