Chris Grayling has rejected the mayor's plans for City Hall to take over suburban rail services.
In an interview with the Evening Standard, Grayling said: "Right now, I think the last thing our railways need in London is deckchair shifting without a clear sign that there is something better on the other side".
Southeastern services across Kent, south east London and parts of East Sussex come up for a new franchise in 2018 and will be expected to include integrated operating teams between train services and infrastructure, as part of Grayling's plans to shake-up Britain's rail network.
The mayor had set out his aims in a business plan, and his arguments for why City Hall and TfL could do a better job of running the capital's trains.
But Khan said he would persist in trying to win the government over to prove why he'd deliver a better service for passengers.
"The only proven way of improving services for passengers is giving control of suburban rail lines to TfL," he said. "This is why the government and previous mayor published a joint prospectus earlier this year. There is cross-party support for this from MPs, assembly members, councils inside and out of London and businesses and their representatives.
Anything short of this simply won't make the improvements desperately needed.
It is a fact, TfL lines have more frequent trains, fewer delays and cancellations, more staff at stations and fares are frozen.
We will keep pushing the government to deliver the rail devolution they have promised and that is needed.