Theo Panagiotoulias, chief executive of Star Alliance, said the group's member airlines support the principle of expanding Heathrow, but questioned whether the current £33 billion proposal is becoming unnecessarily expensive.
Speaking at the Aviation Club in London, Panagiotoulias compared Heathrow's ambitions to buying a luxury car packed with optional extras.
He said: "I'd love to have a fully specced Mercedes-Benz that's top of the line. I don't know if I can necessarily afford it, but I'd like it.
"It's the same parallel.
"I've seen some numbers thrown around and they're eye-watering. We've got to be able to have conversations to determine what's the 'nice to have' and what are the things we must have."
Star Alliance's 26 member airlines account for around one in every six aircraft departing Heathrow. The alliance includes Lufthansa, United Airlines, Turkish Airlines, Air China and Singapore Airlines.
Panagiotoulias said the alliance remains firmly behind Heathrow expansion in principle, but stressed affordability would be crucial.
He said: "We fully support the conceptually.
"We think expansion is the right thing for the market. It's the right thing for the airlines, because the airlines are wanting to grow at Heathrow, but there's no simple solution to this. This is going to cost a lot of money."
His comments add to growing concern among airlines over the cost of Heathrow's expansion plans.
British Airways and Virgin Atlantic, Heathrow's two largest airlines, have both previously warned against excessive costs, while Lufthansa and United are the airport's third and fifth largest carriers respectively.
Heathrow has argued that expansion is inherently expensive because of its location close to London and the engineering challenges involved, including plans to reroute part of the M25 motorway.
However, rival developer Arora Group has proposed a shorter and cheaper alternative runway, which British Airways has publicly backed.
The alternative scheme would initially build a 2,300-metre runway between the M25 and M4 motorways, allowing many narrow-body aircraft to operate before extending it across the motorway at a later date.
Arora argues the phased approach would avoid the immediate cost and complexity of moving the M25, relocating power infrastructure and diverting rivers, while allowing new runway capacity to be delivered sooner.
Panagiotoulias said he was not yet prepared to back either proposal.
He said he wanted to see more detailed information from both Heathrow and Arora before deciding which scheme would best serve airlines.
The comments come just days after Heathrow chief executive Thomas Woldbye dismissed Arora's proposal in his strongest criticism yet of the rival plans.
Woldbye described the alternative as little more than "drawings on the back of an envelope" and insisted Heathrow's proposal for a full-length 3,500-metre runway crossing the M25 remains the only viable option.
He said: "There's no lower-cost option, there are drawings on the back of an envelope, and that's all there is.
"If we want a third runway we need to get on with the scheme on the table."
Arora Group hit back, with founder Surinder Arora arguing Heathrow has become one of the world's most expensive airports because of its poor record on major developments.
He said his company's proposal could still deliver additional runway capacity by the Government's target date of 2035 while offering a more cost-effective solution.
The debate comes after ministers published a draft Heathrow policy that leaves the door open for rival developers to submit competing runway proposals.
While the policy allows construction to be carried out in stages, any successful bidder will still need to secure planning permission for the full-length runway before work can begin.
