It is only 2,500 metres of tarmac but already Heathrow’s proposed third runway has provoked fury among environmentalists, blighted the lives of tens of thousands of people and triggered a fierce political battle that will continue through to the next general election.

The Government’s decision to go ahead with the £9 billion project in the face of opposition from an unlikely coalition of green campaigners, Tory politicians and thousands of potential Labour voters affected by the development will have far-reaching consequences.

Heathrow will finally be granted the expansion that airline chiefs say is essential if the British economy is not to be stifled by the shortcomings of its transport infrastructure. But as the airport grows to allows thousands of additional flights every week, hundreds of homes will be demolished and a wide circle of villages and towns in London and the South East will find themselves blighted by noise and emissions as new flightpaths are established.

In the short term, congestion at Heathrow and its two existing runways will remain acute because its capacity will not increase until the third runway opens. More than a million people living near Heathrow will be spared any increase in aircraft noise until at least 2015 after the Government abandoned a plan for more intensive use of the existing two runways.

Those living under the existing flight paths will still have eight hours of respite a day from aircraft flying overhead. Geoff Hoon, the Transport Secretary, rejected a proposal for “mixed mode”, under which both runways would have been used for take-offs and landings all day. He said that the existing system of runway alternation would be kept, meaning that one runway will be used for all landings and the other for all take-offs, with their roles switching at 3pm each day.

The Government had said previously that it wanted to introduce mixed mode to reduce delays and allow an additional 60,000 flights to use the existing runways.

Mr Hoon said that the new runway would be subject to a limit of 125,000 flights a year, half its capacity, until 2020. The existing cap of 480,000 flights at Heathrow will be raised initially to 605,000. Mr Hoon suggested that he was making a concession to the environmental lobby by leaving the new runway half empty in the early years. However, it emerged that he had no choice because of noise limits previously agreed by the Government.

From 2020, total flights will be allowed to rise to more than 700,000 if the aviation industry can demonstrate that it is meeting a target to reduce climate change emissions from aviation below 2005 levels by 2050. Mr Hoon said that the government-appointed Committee on Climate Change would review in 2020 whether the target was likely to be met.

Greener By Design, a lobby group linked to the aviation industry, said that the target could be met simply by airlines buying modern aircraft that are now under development.

Mr Hoon also said that extra capacity on the new runway would be allocated according to “a new ‘green slot’ approach to incentivise the use at Heathrow of the most modern aircraft”. When asked how this would work, however, the Department for Transport said: “The detail on green slots will be worked up in the future.”

In prebriefings to the media on Thursday, the Government had claimed that it would “promise” to build a high-speed rail line linked to Heathrow. However, it became clear yesterday that it is committing only to carry out another study into a possible line, nine years after commissioning, and then shelving, the last study on the same topic.

Mr Hoon said that he would create a company, High Speed 2, and order it to develop a proposal by the end of the year for a new line between London and the West Midlands, possibly including a “new international interchange station” at Heathrow.

The Civil Aviation Authority, which is funded by airlines, will decide whether noise and air quality limits have been met before the new runway starts operating.

Benedict Southworth, director of the World Development Movement, said: “Dubbing this climate-killing project ‘the green Heathrow’ is the most dangerous greenwash of our times. It’s like calling a new motorway ‘green’ because it has a cycle path.” A plan to create toll lanes on congested motorways was abandoned yesterday. Ministers planned to charge a mileage fee for using the hard shoulder, but decided that road pricing is too politically difficult. They will instead introduce “managed motorways”, under which motorway speed limits will be reduced in busy periods.

The main element of a £6billion road expansion plan will be turning the hard shoulder into a running lane on 520 miles of motorway, including sections of the M1, M3, M4, M5, M6, M20, M23, M25, M27, M60 and M62.

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