The inquiry, announced by Jim Fitzpatrick, the aviation minister, follows complaints from pilots and passengers of nausea, dizziness and other health problems both during and after flights.
Estimates of how many people are affected vary.
The Government’s Committee on Toxicity believes passengers on one in 2,000 flights could be exposed to toxins in cabin air.
Others put the figure higher, including Dr Sarah Mackenzie Ross, a clinical neuropsychologist at University College London, who believed as many as 200,000 passengers a year could be affected.
Pilots had reported bad smells or what they believed was contaminated air on a number of aircraft including the Boeing 757, Airbus 319 and BAe 146.