It was reported over the weekend that TfL is seeking engineers to “lead the way in introducing a new, more sophisticated type of road pricing”, which could include charging motorists who rack up longer journeys more money.
“I am ruling out a pay-per-mile scheme while I am Mayor,” Mr Khan told Times Radio.
“But it’s no secret that the Government, transport officials in London and around the country, have been looking at [it] for some time, in relation to a smarter, streamlined service for a variety of reasons.”
Mr Harper said the Mayor’s website had a “whole bunch of job” roles that were required for City Hall to introduce pay-per-mile schemes in the future.
He told LBC: “If you look at the Mayor of London’s own website for his Project 2030 scheme, he wants to roll out more road user charging schemes, pay-per-mile schemes across London.
“There are a whole bunch of jobs on that website, some of them paying up to £90,000 a year, to do pay-per-mile schemes in the future.”
It comes as the controversial Ulez expansion launched in the capital.
Five million more Londoners were brought into the clean air zone as it was widened to the city’s boundary on Tuesday.
Mr Harper said the Government will be supporting legislation, proposed by Tory peer Lord Moylan, that will mean each London council will have to support new motorist levies before they can be introduced across the capital.
He added: “One of the problems here is that a number of London local authorities don’t support [the Ulez] coming into force, so for the future, we are backing an amendment, a backbench amendment to a piece of legislation which will mean in future any road user charging schemes like this would have to be also backed by London boroughs.
Rishi Sunak also hit out at Labour and Mr Khan, as he said he was opposed to the expansion of Ulez in the capital.
The Prime Minister said: “I think people and families are struggling with the cost of living, that is obvious to everyone.
“And at that time, the Labour Party, the Labour Mayor Sadiq Khan and Keir Starmer are introducing the Ulez charge which is going to hit working families.
“I don’t think that’s the right priority, I don’t think that’s the right thing to do and I wish they hadn’t done it.”