Geoff Hoon took on cross-party critics of the government's Heathrow policy this afternoon as he rejected accusations that a consultation on adding a third runway to Britain's largest airport was a "sham".

In a clear indication that internal dissent within the Labour party has not swayed the prime minister, the transport secretary said that Heathrow needed more capacity. Speaking at a House of Commons debate this afternoon, Hoon said that the third runway would be built if a consultation indicated that it would meet air and noise pollution limits.

"This consultation was not about the need for new capacity at Heathrow. We recognised at the time that this would have implications for people around Heathrow, which is why we made it subject to meeting stringent applications and a commitment not to increase the size of the area significantly affected by aircraft noise." Hoon said he expected to announce the outcome of the consultation before the end of the year.

The shadow transport secretary, Theresa Villiers, said the air and noise pollution study had been rendered pointless by the government's consistently pro-Heathrow stance.

"How does he [Hoon] reconcile his statements that he is in favour of a runway at Heathrow with the fact that consultation has just closed? Surely this consultation has been a complete sham."

Hoon retorted that the previous Conservative government had recognised the need for more capacity at Heathrow in 1995, when the then-transport secretary Lord Mawhinney had argued that there might be a case for a third runway.

Hoon's claim that the government was taking "long-term decisions" for the UK's benefit was attacked by his counterpart. Villiers said expanding Heathrow would endanger the government's 2050 goal of cutting carbon dioxide emissions by 80%. "We have got to take long-term decisions on how we achieve an 80% cut in emissions by 2050. It is Labour that are taking short-term decisions on data that is flawed."

The government's aviation policy also drew criticism from its own backbenchers during the debate. David Taylor, the MP for Leicestershire North West, said proposals for airport expansion, which include a second runway at Stansted, had not factored in the impact of climate change and the disruption to nearby communities.

Fiona Mactaggart, the MP for Slough, said that her constituents had been assured when planning permission was given for Terminal Five that there would be no further runways at Heathrow.

The Conservatives have pledged to block the construction of a third runway and instead build a high-speed railway line, which they argue will undermine demand for domestic flights.

Villiers accused the government of ignoring the case for high-speed rail, which she said could eliminate the need for thousands of domestic air journeys per year. "We can provide a viable, realistic high-speed rail alternative to thousands of flights that are going out of Heathrow."

Malcolm Rifkind, the Tory MP for Kensington and Chelsea, said there "must be a limit" to expanding the airport because of its location next to London suburbs. Rifkind said the government should follow the lead of the mayor of London, Boris Johnson, and commission a new study into building a hub airport in the Thames estuary.

Under the government proposals, a new runway would be built by 2020 and would increase the number of flights from 480,000 per year to more than 700,000. Heathrow currently handles 68 million passengers per year. If a third runway is built, this will increase to 120 million a year.