A new battle looms over a Heathrow third runway – or a second at Gatwick – after the Airports Commission said that additional capacity was needed in the south-east of England. Extra runways at London's two biggest airports are on the shortlist the commission will study before issuing its final recommendation.

The government-appointed independent commission led by Sir Howard Davies set out three options in its interim report: a third runway north-west of Heathrow, favoured by the airport; a second proposal to effectively double an existing runway ay Heathrow, put forward by the unconnected Heathrow Hub group; and a second runway to the south of Gatwick.

The commission said it had concluded there was a need for one net additional runway in the south-east by 2030, and likely demand for a second by 2050.

But Davies said that as both airports agreed there was not yet sufficient commercial demand for both to build new runways, only one of Heathrow or Gatwick's runways would go ahead now, if recommended.

And in a huge boost to Gatwick's chances, Davies made clear he had not been convinced by the arguments made by many in aviation, not least by Heathrow and the London mayor, Boris Johnson, that expansion should only occur at one major "hub" – an airport with enough connecting flights and passengers to support other routes. Davies said London was a different case to other European hubs due to its size and popularity as a destination, and he did not accept there was a simple "hub or no hub" debate.

The Thames estuary airport proposal, backed primarily by Johnson, has not been included on the shortlist, although the commission said it would undertake further study of the Isle of Grain option in the first half of 2014 to reach a view later next year whether that option could in fact be shortlisted – a concession apparently won in the last week.

In response to questions about the reprieve for that option – believed to have been desired by the prime minister and chancellor to avoid an early row over Heathrow, as well as the mayor – Davies did not deny meeting senior figures and limited his response to saying: "The shortlist did not change."

While Johnson was quick to describe the lifeline for his plan as still pitting Heathrow against the Thames estuary, Davies made clear that his plan for a new airport was at the margins of his thinking for its vast expense and problems with wildlife, surface access and the closure of existing facilities. : "The notion of a once-in-a-century new development is imaginative," he said.

The commission will request and examine detailed proposals for all of the options, and will give its final recommendation after the next general election.

Launching the report, Davies said: "Decisions on airport capacity are important national strategic choices and must be based upon the best evidence available. The commission has undertaken a fresh, comprehensive and transparent study of the issues. This report is the product of extensive consultation, independent analysis and careful consideration by the commissioners.

"The UK enjoys excellent connectivity today. The capacity challenge is not yet critical but it will become so if no action is taken soon, and our analysis clearly supports the provision of one net additional runway by 2030. In the meantime we encourage the government to act on our recommendations to make the best of our existing capacity.

"The commission will now focus on the challenge of appraising the three options, further assessing the case for a new airport in the Thames estuary, and delivering a robust final recommendation to government in summer 2015."

The other most high-profile omission from the shortlist is Stansted airport, whose owners, MAG, had supported proposals for expansion, but whose potential for major development into a four-runway hub had been primarily promoted by Johnson as an alternative to his estuary plan.

Davies said: "Stansted is only half full and has a lot of room to expand whereas Gatwick is 85% full. Demand has shown it is a lot more popular with airlines and passengers at the moment."

He said the second extra runway he believed necessary by 2050 would probably not be at Heathrow: "The balance between hub and no hub has shifted to point to point so I would be surprised if it was Heathrow but certainly haven't ruled it out."

Although the coalition scrapped plans for a Heathrow third runway in 2010, pressure from business groups and the aviation industry convinced Downing Street to re-examine the issue, and the commission was formed in November 2012.

West London Tory MPs, in particular, have been infuriated by developments, with one, Zac Goldsmith, saying that to back Heathrow expansion would be an "off-the-scale betrayal". Ministers insist David Cameron's pledge not to build additional runways was for this parliament only and any decision will be made after 2015.

Colin Matthews, the Heathrow chief executive, issued a cautious welcome but said it was only an interim shortlist. He added that any recommendation would "need broad support and political leadership once the commission has finished its report to make something happen".

Davies has reduced the extent of possible blight by naming specific options at each airport. The north-west option at Heathrow – one of three possible locations the airport had put forward – would mean the demolition of the village of Harmondsworth, and has been described as the worst possible option for residents of Sipson, which would be spared from demolition but be overflown at the tip of the runway.

The second Heathrow proposal, from the Heathrow Hub firm, which hopes to develop land to the north into an integrated transport hub, would extend the existing northern runway to at least 6km (almost 4 miles), potentially enabling it to operate as two independent runways – a surprise inclusion on the shortlist.

The commission has also put forward some short-term options to improve the operational efficiency of UK airports and airspace, including revised air traffic practices and better road and rail access to existing airports.