He accepted that Mr Cameron, under political attack from Labour for getting rid of the 50p rate, would not appreciate his public call for another tax rate.
“It’s a difficult time, and I accept that people won’t like to hear it, but it’s the kind of point that you’ve got to make as Mayor of London which isn’t necessarily welcome in No 10,” Mr Johnson said.
It was the second time during the conference the mayor has openly differed with the Prime Minister, having earlier this week backed a return to academic selection in state school entry.
Mr Johnson is regarded by some Conservative MPs as a potential leader of the party, but would have to return to the Commons in order to take the post.
He insisted that he will not seek election as an MP before his mayoral term ends in 2016
But he repeatedly refused to rule out seeking a Commons seat after that, saying: “By that stage, it’s really very difficult to say what I’ll be doing ... that is an awful long time in politics.”
Mr Johnson was interviewed after his main conference speech, in which he poked fun at Mr Cameron but backed the Prime Minister to lead Britain to economic recovery and win the next general election.
Mr Cameron was in the hall to hear Mr Johnson praise his economic leadership.
“I know that David Cameron will win in 2015, when the economy has turned around and people are benefiting in jobs and growth from the firm leadership and the tough decisions you have taken,” Mr Johnson said.
Ministers including Kenneth Clarke have said Mr Johnson should “calm down” and try to end speculation about his future.
Mr Johnson said he agreed, adding that he wanted to focus on his work in London. “Actually I would welcome the spotlight moving away,” he said.
Still, his call for a tax cut will only reinforce his appeal to free-market Conservatives. The mayor’s suggestion was echoed by Lord Forsyth, a former Cabinet minister.
Lord Forsyth, who once advised George Osborne on tax policy, said that the Chancellor has failed to cut and simplify taxes since taking office.
“He’s complicated the system and he hasn’t taken the action which is necessary to broaden the tax base and lower it,” the peer said.
“Cutting the top rate to 40 per cent “would mean more money and therefore less pressure on lower-paid people”, he said.