The newspaper maintained she had told a reporter it was "much more important" to expand Heathrow than Stansted.
This was due, the newspaper claimed, to the "economic benefits of adding capacity at Britain's only hub airport, which has flights to all the major countries".
But Friday's Times carried a letter from Kelly stating that the newspaper's headline was "wrong".
Kelly wrote: "In 2003, against the background of increased demand for air travel, the Government examined the balance between the economic benefits in terms of jobs and growth and its environmental impact.
"We concluded there was a need for two new runways in the South East, at Stansted and at Heathrow.
"This position has not changed, and yesterday I launched a public consultation on proposals for a third runway at Heathrow."
Kelly concluded by saying she understood the owners of Stansted airport would be submitting a planning application for a second runway in "the near future".
Adding Capacity at Heathrow Airport - the consultation paper launched Thursday into the expansion of Heathrow airport - is available by clicking here.