Opponents of the expansion claim BAA has been given an unfair advantage by having early access to key technical data on air pollution.
They want the preliminary results to be made available to the public.
But the DfT said the data would not be released until the study was ready to go out to public consultation.
Tainted study
The department confirmed it has been working with BAA on assessing the environmental impact of a third runway.
It said a public consultation on the proposals was expected to begin before the end of the year.
"The government now runs the risk that the results of its air pollution studies will be tainted"
2M, a group of 12 local authorities affected by the plans, said the government study appeared to be less than independent.
"Giving the results first to BAA just gives them a head start on everyone else," said Edward Lister, of Wandsworth Council, on behalf of 2M.
"The government now runs the risk that the results of its air pollution studies will be tainted.
"This will be a huge embarrassment for the DfT and further confirmation to the public of the lengths the department will go to in its efforts to 'prove' Heathrow can meet its air pollution targets."
The group is calling on Cabinet Secretary Sir Gus O'Donnell to investigate claims that the DfT has broken civil service rules by sharing data with BAA.
But the DfT has rejected any wrongdoing saying the 2003 Air Transport White Paper made it clear that BAA should work with the government on proposals for a third runway.
"It would not have been sensible or possible to attempt this work without the technical and operational expertise of the airport operator," said a DfT spokesman.
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