Members of York Council's Gambling, Licensing and Regulatory Committee tonight debated for more than two hours over Uber Britannia Limited's application.
The company's current 12-month licence is due to expire on Christmas Eve.
Councillors concluded that the taxi-hailing firm was not a fit and proper person - a required condition to refuse an application of its kind.
A spokesperson for York Council said: “The application by Uber Britannia Ltd to renew its private hire operator’s licence in York has been considered by City of York Council’s Gambling, Licensing and Regulatory Committee tonight.
“Applying the legislation, the committee has decided to refuse the application having concerns about a data breach currently under investigation and the number of complaints received."
Speaking after the meeting Neil McGonigle, general manager for Uber in York, said the company would now review the details of the decision.
He said: “This is a disappointing vote for the riders and drivers who use our app in the city.
"More choice and competition is a good thing for both consumers and licensed drivers in the area.
"Passengers tell us they love being able to track their car on a live map, pay without cash and get a receipt with their fare and the route taken.
"Licensed drivers partner with us because with Uber they can choose if, when and where they drive. We will review the details of the decision once we receive the formal notice from the council.”
The firm's appeal against that decision in London will be heard by Westminster Magistrates’ Court in Spring next year. Uber Britannia Limited can lodge an appeal with the Magistrates' Court over the latest decision by York Council.
Coun Sonja Crisp tabled a motion to refuse the application on the basis of the data breach that affected the 57 million customers and drivers in 2016.
The second reason for refusal related to complaints made against the firm in York.
The decision is the latest blow to hit the taxi-hailing company, after Uber had its licence suspended in Sheffield this week.
Since December 2016, 296 complaints were made relating to hackney carriage and private hire vehicles or drivers in York up to November 22.
York Council said 155 of these complaints related to Uber vehicles or drivers.
But only four related to an Uber vehicle or driver licensed by the council - and 129 were made against those licensed by other local authorities, leading to councillors raising questions about the number of Uber drivers coming from outside York to work in the city.
Coun Dave Taylor, a member of the committee, said during the meeting: "This city needs to have control of its taxi services and it needs to have a level playing field and I don't know if that means then national legislation aught to be tidied up.
"But I don't think that we can license a company which directs drivers to go around the houses, pumping up fair for customers, that tries to claim it has no liability for any claims, demands or losses, which claims to have a local office but never seems to staff it and the number of complaints against them is so high.
"I think those are the grounds on which we can refuse this licence."
Neil McGonigle, Uber Head of Cities, North of England, spoke in support of Uber at the meeting.
He revealed that some 28,000 have used the company's app in York in the last three months.
Mr McGonigle said: "From our experience the passenger like the ability to press a button to request a car, take a trip without having to use cash at all and from a safety point of view, being able to track every element of that journey real-time.
"Whether that's themselves, family members, friends or whatever through the app."
He said people from 73 different countries are now using the app in York, as Uber has recently taken on more international visitors in York.
The meeting was told licenses for Uber to operate had been refused in Reading, North Tyneside and Cardiff.
Saf Din, chairman of York Hackney Carriage Association said he does not object to competition, but that Uber was not a "fair player" in the public transport game.
Ahead of the decision, Mr Din told the meeting: "I urge you to be the most active members by refusing the application and offer no licence until you are fully satisfied."
He also handed over a petition regarding safeguarding of passengers, objecting to Uber's licensing renewal.
Speaking during the debate tonight, Coun Suzie Mercer said: "I was still undecided having read the papers and I'm still undecided.
"Everyone is just trying to do a job, you've got good apples nad bad apples in all trades.
"Uber is used all over the world by millions of people. In York it's mainly the young people who use it and I think maybe as well it's probably a young thing.
"Out of town drivers wouldn't come if there wasn't any work and we must remember that if the public want it, then who are we to deny it?"