The London mayor, Boris Johnson, has launched a withering attack on the "irrelevant" and "myopic" Airports Commission, after the panel set up to decide where to build additional runways in the south-east finally ruled out his plan for a new hub in the Thames estuary.

The verdict leaves only Gatwick and Heathrow on the final shortlist for the commission's ultimate recommendation for additional runway capacity in south-east England.

Johnson said the decision was looking like "a smokescreen for a U-turn on Heathrow".

In comments aimed at putting pressure on the government, he said: "We were all of us, David Cameron and I, elected on a pledge to stop a third runway and my first job is to make sure we stick to our manifesto pledges."

The commission said that after a detailed study it had concluded that the proposal for a new four-runway airport had "substantial disadvantages that collectively outweigh its potential benefits".

The commission chairman, Sir Howard Davies, said there were serious doubts about its operation and "deliverability".

"The economic disruption would be huge and there are environmental hurdles which it may prove impossible, or very time‑consuming to surmount," he said. "Even the least ambitious version of the scheme would cost £70bn to £90bn, with much greater public expenditure involved than in other options – probably some £30bn to £60bn in total."

He added: "There will be those who argue that the commission lacks ambition and imagination. We are ambitious for the right solution. The need for additional capacity is urgent. We need to focus on solutions which are deliverable, affordable, and set the right balance for the future of aviation in the UK."

Despite the pre-emptive defence, Johnson said the commission seemed to have no single reason to rule out an estuary airport and appeared unable to recommend it simply because of its sheer scale and vision. He warned that a third runway at Heathrow would run into immovable political opposition again.

Johnson said: "In one myopic stroke the Airports Commission has set the debate back by half a century and consigned their work to the long list of vertically filed reports on aviation expansion that are gathering dust on a shelf in Whitehall.

"Gatwick is not a long-term solution and Howard Davies must explain to the people of London how he can possibly envisage that an expansion of Heathrow, which would create unbelievable levels of noise, blight and pollution, is a better idea than a new airport to the east of London that he himself admits is visionary."

The mayor claimed Davies had told him that the single additional runway at Heathrow and Gatwick would not be enough for the long term "and in 2020 you're going to have to think again".

Johnson said he blamed Whitehall for blocking the estuary airport, rather than the commission, and called on other politicians to "come out of their foxholes" and "man up". "What I'd like to hear is other politicians actually come forward with some of the vision and the clarity that we've come forward with our proposals for solving the airport problem. I think that is, in my view, a very temporary setback. I think what people need to do is man up … and come out with what they are proposing as the solution."

Speaking on the BBC Radio 4 Today programme, Davies said the estuary airport plan was too risky, with immense logistical challenges, complicated surface access requirements and environmental problems, and that he suspected it would never have been built.

"Ambition is a great thing. We've spent 18 months looking at whether this thing could work. Unfortunately one has to look at the practicality and cost benefit."

He denied the commission had made its final choice, saying: "There are many uncertainties still on which we are consulting. We want to make a decision that will stick."

The mayor has faced criticism from the London assembly over the time and funds devoted to the scheme, nicknamed "Boris island".

The Labour group's Val Shawcross said Johnson had "wasted more than £5m of taxpayer money pursuing this pie-in-the-sky vanity project".

"If anything, Londoners now deserve an apology from their mayor."

Mary Creagh MP, Labour's shadow transport secretary, said: "This back-of-a-fag-packet scheme was designed less for the country's economic future and more for the omnishambles mayor's political ambitions."

But Johnson said his team would continue to make the case, and that he could revive his estuary plans as an MP.

A Gatwick spokesman said the commission's decision was an important juncture. The airport's chief executive, Stewart Wingate, said: "Now Britain's choice is clear: expand Gatwick and support genuine competition, lower fares and greater choice for passengers, or expand Heathrow and return to the stale monopoly of the past and watch the cost of going on holiday, travelling for business and exporting goods and service go up."

Heathrow's chief executive, John Holland-Kaye, repeated his entreaty of last week to Johnson, saying: "We have always agreed with the mayor that Britain needs a successful hub airport to compete in the global race for jobs and growth. Heathrow is now the only hub left in the race. We would like to work with the mayor to deliver Heathrow expansion in a way that benefits the whole country while reducing noise impacts for local people."

The mayor, now prospective MP for nearby Uxbridge and South Ruislip, where many constituents work at the airport, did not repeat his calls to close Heathrow entirely.