Sir Howard Davies, who launched his inquiry last week, says he wants a public debate first and foremost about the issues surrounding airports.
Davies, a former head of the Financial Services Authority, was responding to attempts by the London mayor to ambush the launch of the three-year commission last Friday by publicly complaining that the process was too slow.
Davies has been appointed by David Cameron to report on how the UK can maintain its position as Europe's major air hub – but not until after the next general election in 2015.
Johnson also insisted that one of the main options set to be examined by Davies's commission in a bid to increase capacity – a third runway at Heathrow – "simply will not happen" because of the noise pollution it would cause to Londoners and the political impact it would have.
In his first newspaper interview, Davies responds to the Tory mayor's criticisms, insisting that a third runway will "stay on the table", laments the terms of the debate and says he is determined to ignore the "swirling" political row over the issue.
"Obviously we have to have a public process here, but the public process I want is about the issues rather than about the timing and the politics," he says. "But, hey, that is not something I can deal with."
He adds: "I don't think we can afford them [the politics] to be [involved], quite frankly. I think the whole point of asking an independent commission to do this is in order not to do that. I observe the political debate swirling around this, but I don't think it makes sense to get involved in it."
Cameron also chose on Saturday to slap down Johnson, who wants a new airport to be built in the Thames estuary and for the development of Heathrow to be swiftly ruled out.
The prime minister urged Johnson to respect the fact that Davies had "a completely open mind" on the issue. "What I would say to Boris, what I have said to Boris, is that for the first time a government has properly put all the options, including estuary options, on the table," Cameron said.
"Boris is passionate about the idea of an estuary airport. Now he has a forum in which to put forward his arguments in a way in which he hasn't in the past."
The future of Britain's airports has been contentious for a number of years, but has been a particularly rancorous issue since the London mayor proposed an alternative "Boris island" in the Thames.
The Observer understands that Boris has privately told the chancellor, George Osborne, that his assistance at the next general election cannot be guaranteed if the commission sticks to its timetable. He has also committed himself to causing trouble over the issue, including a possible bid for a judicial review into the commission's role in the process.
In the interview, Davies says "all options are on the table", but reveals he had insisted to the prime minister that his commission was able to shortlist the options for an increase in capacity by 2013. He said this would allow the more imaginative ideas such as "Boris island" to receive extra scoping work after 2013 by the commission if they were found to have potential. Davies also:
■ Denies that his views on climate change had been influenced by his former boss, the climate change sceptic Lord Lawson, but refuses to elaborate, describing his personal views on global warming as irrelevant because he will comply with the government's commitment to cut carbon emissions by 80% by 2050.
■ Sounds the death knell for the prime minister's plans for a happiness or quality of life index to have a role in public policy-making, adding that he didn't "quite know what they mean really".
■ Admits that he "can't be convinced" that the politicians will act on his report in 2015, although it would "be the most obvious thing for them to do".
■ Reveals that he is interested in the airport at Chicago because "they had a huge, long debate about an extra runway in Chicago where there was a lot of opposition, and eventually they decided to go for it. So we are going to look at how that worked."
■ Says he had visited Hong Kong, where a mountain was dismantled to create a new island airport, but was advised "don't do it the way we did".
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