McLoughlin said he "hoped" that the Government would be in a position to choose between the options at Heathrow and Gatwick by next summer.
The comments risk a fresh backlash after ministers were branded "gutless" for ordering extensive new analysis.
David Cameron had promised a decision on the issue by Christmas after the detailed review by Sir Howard Davies concluded that a new runway at Heathrow was the best of three shortlisted possibilities.
Mr McLoughlin told BBC Radio 4's Today programme the Government had made "some important moves" by accepting the case for additional capacity in the South East.
But he insisted it was important to carry out more research on the environmental impact.
"Even Commons select committees are saying that we should take into account some of the changes that have come about since Sir Howard Davies published his report," Mr McLoughlin said.
"We accept that additional airport capacity is needed and we will make a decision on that hopefully in the summer of next year."
Pressed on why he was only "hopeful" that the decision would be taken in the summer, Mr McLoughlin said: "The summer of next year would still allow us to get the extra capacity we need by 2030...
"I believe that by the summer of next year we will be in a position to have done the extra work which I will be doing as Secretary of State for Transport with the Department for Transport and with the promoters of the three schemes.
"I hope that we will be able to make a firm recommendation to the Cabinet sub-committee next summer. I hope that we will be. We should be in that position."
Mr McLoughlin urged people not to "fixate" on proposals for a third runway at Heathrow, saying the options of extending an existing Heathrow runway and building a second runway at Gatwick were "still on the table".
"Please get off the fixation of a third runway, because it could be a second runway. It could be a second runway at Gatwick," he said.
The announcement of the delay was welcomed by environmental groups and local campaigners.
But critics said it was a politically-inspired move to avoid damaging resignations by high-profile Tories - including London mayoral candidate Zac Goldsmith, who has vowed to quit as an MP if a Heathrow plan is approved.
The contest to succeed current City Hall incumbent Boris Johnson - himself implacably opposed to the £18.6bn third runway project - will take place in May, with Labour candidate Sadiq Khan also against Heathrow expansion.
John Longworth, director-general at the British Chambers of Commerce, said: "Businesses will see this as a gutless move by a Government that promised a clear decision on a new runway by the end of the year.
"Business will question whether ministers are delaying critical upgrades to our national infrastructure for legitimate reasons, or to satisfy short-term political interests. Ministers need to stop prevaricating and get on with doing what the country sorely needs."
The CBI, which condemned the "deeply disappointing" delay, has warned waiting could cost the economy more than £5bn.
The Board of Airline Representatives in the UK said it was "inconceivable that the Government has had insufficient time, or a lack of information, to make the decision it long promised".
A spokesman said: "Every week that passes has a direct cost to the UK economy, its international connectivity and reputation."
A delighted Mr Goldsmith said the Government had "heard the arguments, seen sense and will judge the options against an environmental test".
"There can be no doubt that in a fair contest on air quality, Heathrow will not win," he added.
Mr Johnson said the Heathrow runway plan was "officially grounded" and revived calls for a new airport in the Thames Estuary, dubbed "Boris Island".
Gatwick's chief executive, Stewart Wingate, said the delay was a "defining moment in the expansion debate" and claimed Heathrow's supporters must now realise that a third runway will never go ahead "as the environmental hurdles are just too high".
But Heathrow chief executive John Holland-Kaye insisted he was "confident we can meet tough environmental standards".
The shortlist of proposals being considered by the Government also features a plan to extend the existing northern runway at Heathrow to form the equivalent of two runways.
Shadow transport secretary Lilian Greenwood said the statement "owes more to political calculations than genuine concern for the environment or residents who now face another year of blight and uncertainty".
Labour former cabinet minister Andrew Adonis said: "I welcome the fact that the Government has accepted the case for an extra runway at Heathrow or Gatwick, as recommended by the independent Airports Commission.
"It is right that the decision should be taken on the basis of the latest data on environmental impacts, and the Government has committed to complete this work by the summer.
"It is vital that a decision on a new runway is now taken within months. A decision to go ahead in 2016 will make it possible to build the runway by 2030 as recommended by the Airports Commission, but any further delay beyond next summer will jeopardise jobs and growth."