Mr Patrick McLoughlin said the decision will not be made until "October at the earliest".
An announcement was expected to be made this summer, but after Britain decided to leave the EU the decision is to be made by the new prime minister, after David Cameron said he is to step down.
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However, the airport's Chief Executive Mr Holland Kye, said that a third runway must be a part of the Government’s Brexit plan.
He said: "If Britain wants to be confident, outward-looking and at the centre of the world’s economy then expanding Heathrow must be a key building block in the Government’s Brexit plan.
"It will allow British exporters to trade with all the growing markets of the world, strengthening Britain’s position as one of the great trading nations. And at a time of uncertainty a £16bn privately funded infrastructure investment will create jobs and growth across the UK.
"Government can send the strongest possible signal that Britain is open for business and confident in its future by expanding Heathrow."
(CD/MH)
