London Mayor Boris Johnson has reacted with fury to a decision of the Government-appointed Airports Commission to reject the “Boris Island” Thames Estuary airport plan.

Mr Johnson said: “In one myopic stroke the 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.”

The thumbs-down for the four-runway estuary scheme leaves the commission, headed by Sir Howard Davies, with three shortlisted schemes - two involving expansion at Heathrow Airport in west London and the other for a new runway at Gatwick in West Sussex.

Mr Johnson said: “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, and which would create the jobs and growth this country needs to remain competitive.

“It remains the only credible solution, any process that fails to include it renders itself pretty much irrelevant, and I’m absolutely certain that it is the option that will eventually be chosen.”

An added complication for Mr Johnson is that he is now seeking the Tory 2015 general election candidacy at Uxbridge and South Ruislip - a constituency which borders Heathrow and contains many people who depend on the west London airport for their livelihood.

The estuary scheme was ruled out after the commission said the proposal had “substantial disadvantages that collectively outweigh its potential benefits”.

Sir Howard said: “We are not persuaded that a very large airport in the Thames Estuary is the right answer to London’s and the UK’s connectivity needs.

“While we recognise the need for a hub airport, we believe this should be a part of an effective system of competing airports to meet the needs of a widely spread and diverse market like London’s.”

The Heathrow and Gatwick options had been shortlisted by the commission last December, with Sir Howard announcing that further studies would be made on the estuary plan with a decision towards the end of 2014.

Today, Sir Howard, the former head of the Financial Services Commission, said: “There are serious doubts about the delivery and operation of a very large hub airport in the estuary.

“The economic disruption would be huge and there are environmental hurdles which it may prove impossible or very time-consuming to surmount.”

He went on: “Even the least ambitious version of the scheme would cost £70 to £90 billion with much greater public expenditure involved than in other options - probably some £30 to £60 billion in total.

“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.”

The commission is due to make its final report to ministers in summer 2015 - after the general election.

Later, Sir Howard told the BBC Radio 4 Today programme: “We think it’s (the estuary scheme) too risky. The logistical challenges of shifting an airport 17 miles across London are immense. The surface access requirements to it are very complicated and we simply think that there’s a strong chance that you would never actually get it built.”

Shadow transport secretary Mary Creagh said: “Boris Johnson’s fantasy island airport plan, which would have closed Heathrow and caused longer passenger journeys, has finally been dashed.

“Time and public money should never have been spent on his vanity project whose costs have been put at up to £100 billion.

“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.”

Members of Medway Council in Kent were pleased with the commission’s announcement.

Council leader Rodney Chambers said: “I am pleased our campaign to stop the estuary airport has been successful.

“We have said all along that it should never have even been considered. The cost to the taxpayer was never fully explained and it would have resulted in the mass destruction of habitat and wildlife that could never be replaced.”

Nathan Stower, chief executive of the British Air Transport Association, said: “Britain needs additional runway capacity in the South East of England, but not at any price.

“With the Thames Estuary option sensibly ruled out for good, the commission is free now to concentrate on scrutinising the business cases of the three shortlisted options.”

Back Heathrow campaign co-ordinator Rob Gray said: “This decision is a major victory for the thousands of local residents in west London who had begun to fear the worst.”

Gatwick Airport chief executive Stewart Wingate said: “This is an important juncture in the aviation debate because 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.”