Theresa May has said the decision not to renew Uber’s London licence is disproportionate, and accused the mayor, Sadiq Khan, of putting thousands of jobs at risk.

The ride-hailing company to appeal against the decision by Transport for London not to renew its licence to operate in the capital for reasons of public safety.

The prime minister acknowledged there were “safety concerns for Uber to address” but said the decision “damaged the lives” of millions of users.

The licence expires on 30 September, although Uber will continue to run cars during the appeal process, which could last a year.

Speaking before the Conservative party conference, May told the BBC: “At a stroke of a pen, what the mayor has done is risked 40,000 jobs and of course … damaged the lives of those 3.5 million Uber users.

“Yes there are safety concerns and issues for Uber to address, but what I want to see is a level playing field between the private firms and our wonderful London taxis, our black cabs, our great national institution.”

She added: “I think a blanket ban is disproportionate. What I think people want to see is choice.”

Uber’s new chief executive, Dara Khosrowshahi, apologised in an open letter on Monday for the company’s mistakes in London and promised it would change.

The former Expedia chief wrote: “While Uber has revolutionised the way people move in cities around the world, it’s equally true that we’ve got things wrong along the way. On behalf of everyone at Uber globally, I apologise for the mistakes we’ve made.

“We will appeal [against] the decision on behalf of millions of Londoners, but we do so with the knowledge that we must also change.”

Khan, who is also chair of TfL, welcomed the apology and urged London’s transport regulator to meet Khosrowshahi.